ct.models.pipeline.Pipeline gives different predictions than it's models run consecutively

## 🐞Describing the bug
The bug became apparent when we were trying to export a detection model to CoreML, using `ct.models.pipeline.Pipeline` to combine the detector (which outputs raw xywh boxes and confidences) and NMS model. The resulting pipeline model is giving incorrect predictions.

However when we take the pipeline's models separately and run NMS model on the detector predictions the results are correct.

## To Reproduce
```
import tensorflow as tf
import coremltools as ct
from PIL import Image

# Constructing dummy yolo-like model,
# when we pass a completely black (0's) image through it
# we will get all the coordinates and confidences equal to 0.5 due to sigmoid(0.)

n_classes = 34
n_anchors = 4032

inputs = tf.keras.Input(shape=(256, 256, 3), name='image')

confidences = tf.keras.layers.GlobalAveragePooling2D()(inputs)
confidences = tf.keras.layers.Dense(n_classes * n_anchors, activation='sigmoid')(confidences)
confidences = tf.keras.layers.Reshape((n_anchors, n_classes))(confidences)
confidences = tf.squeeze(confidences, axis=0)

coordinates = tf.keras.layers.GlobalAveragePooling2D()(inputs)
coordinates = tf.keras.layers.Dense(4 * n_anchors, activation='sigmoid')(coordinates)
coordinates = tf.keras.layers.Reshape((n_anchors, 4))(coordinates)
coordinates = tf.squeeze(coordinates, axis=0)

dummy_detector = tf.keras.Model(inputs=inputs, outputs=[confidences, coordinates])

input_shape = [1] + dummy_detector.input.shape[1:].as_list()

detector_model = ct.convert(
dummy_detector,
inputs=[ct.ImageType("image", shape=input_shape)],
convert_to="mlprogram",
)

# Constructing NMS model

nms_spec = ct.proto.Model_pb2.Model()
nms_spec.specificationVersion = 5

for i in range(2):
decoder_output = detector_model._spec.description.output[i].SerializeToString()

nms_spec.description.input.add()
nms_spec.description.input[i].ParseFromString(decoder_output)

nms_spec.description.output.add()
nms_spec.description.output[i].ParseFromString(decoder_output)

nms_spec.description.output[0].name = "confidence"
nms_spec.description.output[1].name = "coordinates"

output_sizes = [n_classes, 4]
for i in range(2):
ma_type = nms_spec.description.output[i].type.multiArrayType
ma_type.shapeRange.sizeRanges.add()
ma_type.shapeRange.sizeRanges[0].lowerBound = 0
ma_type.shapeRange.sizeRanges[0].upperBound = -1
ma_type.shapeRange.sizeRanges.add()
ma_type.shapeRange.sizeRanges[1].lowerBound = output_sizes[i]
ma_type.shapeRange.sizeRanges[1].upperBound = output_sizes[i]
del ma_type.shape[:]

nms = nms_spec.nonMaximumSuppression
nms.confidenceInputFeatureName = detector_model._spec.description.output[0].name
nms.coordinatesInputFeatureName = detector_model._spec.description.output[1].name
nms.confidenceOutputFeatureName = "confidence"
nms.coordinatesOutputFeatureName = "coordinates"
nms.iouThresholdInputFeatureName = "iouThreshold"
nms.confidenceThresholdInputFeatureName = "confidenceThreshold"

nms.iouThreshold = 0.35
nms.confidenceThreshold = 0.1

nms.pickTop.perClass = True

nms_model = ct.models.MLModel(nms_spec)

# Constructing pipeline model

pipeline_model = ct.models.utils.make_pipeline(detector_model, nms_model)

# Predictions

img = Image.new(mode='RGB', size=(256, 256), color=0)
print("Pipeline predictions:")
# There should be one box only and no zeros in confidences (as none are in the NMS input)
print(pipeline_model.predict({'image': img}))

detector_from_pipeline = ct.models.MLModel(
pipeline_model._spec.pipeline.models[0],
weights_dir=pipeline_model.weights_dir
)

nms_from_pipeline = ct.models.MLModel(
pipeline_model._spec.pipeline.models[1]
)

print("Individual models consecutive prediction:")
# Correct behavior
print(nms_from_pipeline.predict(detector_from_pipeline.predict({'image': img})))
```

Output (both pipeline predictions and individual models' predictions should be the same):
```
Pipeline predictions:

{'coordinates': array(
[[0.5, 0.5, 0.5, 0.5],
[0.5, 0.5, 0.5, 0.5],
[0.5, 0.5, 0.5, 0.5],
[0.5, 0.5, 0.5, 0.5],
[0.5, 0.5, 0.5, 0.5],
[0.5, 0.5, 0.5, 0.5],
[0.5, 0.5, 0.5, 0.5],
[0.5, 0.5, 0.5, 0.5]],
dtype=float32),
'confidence': array([[0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0. , 0. , 0. , 0. , 0. , 0. ,
0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
[0. , 0. , 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ,
0. , 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[0. , 0. , 0. , 0. , 0. , 0. , 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[0. , 0. , 0. , 0. , 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]], dtype=float32)}

Individual models consecutive prediction:

{'coordinates': array([[0.5, 0.5, 0.5, 0.5]], dtype=float32),
'confidence': array([[0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]], dtype=float32)}
```

## System environment (please complete the following information):
- coremltools version: 8.2 (also happens on 7.2)
- OS (e.g. MacOS version or Linux type): MacOS 15.1
- Any other relevant version information (e.g. PyTorch or TensorFlow version): Tensorflow 2.12.0 (also happens on 2.13.0)

## Summary:
* If we use full model as a pipeline: `pipeline_model.predict({'image': img})` we get incorrect results
* However, if we split the pipeline into two calls: `nms_from_pipeline.predict(detector_from_pipeline.predict({'image': img}))` the results are correct.
* Also we noticed that for smaller number `n_classes` e.g. 1, 2 the code works as expected
* Question: are we using NMS correctly? We weren't able to find any explicit documentation, so we based this on how it is implemented in other repos (https://github.com/cloud-annotations/cloud-annotations/blob/main/training/scripts/trainer/src/convert/build_nms.py, https://github.com/hietalajulius/yolov5/blob/1023da95a54466cc320d79cc0408ea8b171d0321/export-nms.py#L237)

Start by running the supplied TensorFlow and Core ML reproduction, focusing on ct.models.utils.make_pipeline and the nonMaximumSuppression model configuration. Compare pipeline_model.predict with the two consecutive predict calls, especially for n_classes=34 versus smaller class counts. Done means the pipeline produces the same filtered confidence and coordinate outputs as the consecutive models.

Written by the indexing model from the issue text.