Converting TileMap to TileMapLayer adds extraneous Property (use_kinematic_bodies) in .tscn file

### Tested versions

- Reproducible in 4.4.1
- Ubuntu 20.04.6 LTS

### System information

Godot v4.4.1.stable - Ubuntu 20.04.6 LTS (Focal Fossa) on X11 - X11 display driver, Multi-window, 1 monitor - Vulkan (Forward+) - integrated Intel(R) UHD Graphics (CML GT2) - Intel(R) Core(TM) i7-10710U CPU @ 1.10GHz (12 threads)

### Issue description

I was re-creating a demo-project manually, in 4.4.1, and created a TileMapLayer (after seeing that TileMap was deprecated), but it didn't work like the demo I was copying. Looking further, the demo-project was 4.3, and I had converted it to 4.4.1, to compare, and discovered some anomalies in the newly node-transformed TileMapLayer. It had the property `use_kinematic_bodies = true` in two places, in the .tscn file, and when I checked/unchecked the Property checkbox in the Editor tab, it removed only one of them. So there was a case where the .tscn file had the property set to True, but in the Editor, it showed as unchecked. (Took me a long time to debug that, comparing my broken project to the working demo-project, too).

```
$:~/Code/test/book_jungle_jump$ grep -rni use_kinematic_bodies .
./moving_platform.tscn:11:use_kinematic_bodies = true
./moving_platform.tscn:17:use_kinematic_bodies = true

```

### Steps to reproduce

Step 0: get initial, unconverted TileMap

git checkout Step-0-PreConvertTileMap

- note that there is a TileMap, with "collision_animatable=true".
- I'm not sure that's required, it seemed to generate the property either way

Step 1: Extract TileMap Layers

either manually do:

- Select TileMap
- click toolkit "Extract TileMap layers as individual TileMapLayer nodes"

or

git checkout Step01-ExtractTileMap-Layers

Step 1 Results:

There is a "use_kinematic_bodies = true" in the .tscn file

git diff moving_platform.tscn

+[node name="Layer0" type="TileMapLayer" parent="TileMap"]
+use_parent_material = true
+tile_map_data = PackedByteArray(0, 0, 0, 0, 0, 0, 0, 0, 15, 0, 14, 0, 0, 0, 1, 0, 0, 0, 0, 0, 17, 0, 14, 0, 0, 0, 2, 0, 0, 0, 0, 0, 17, 0, 14, 0, 0, 0, 3, 0,
+tile_set = ExtResource("2_iov41")
+use_kinematic_bodies = true

Step 2: Convert TileMap to TileMapLayer

either manually do:
- Select TileMap
- right-click->Change Type->TileMapLayer

or
git checkout Step02-ConvertTileMap-to-TileMapLayer

Step 2 Results:

There is a "use_kinematic_bodies = true", although in the Editor, the checkbox is not checked.

$ tail -6 moving_platform.tscn

[node name="Layer0" type="TileMapLayer" parent="TileMap"]
use_parent_material = true
tile_map_data = PackedByteArray(0, 0, 0, 0, 0, 0, 0, 0, 15, 0, 14, 0, 0, 0, 1, 0, 0, 0, 0, 0, 17, 0, 14, 0, 0, 0, 2, 0, 0, 0, 0, 0, 17, 0, 14, 0, 0, 0, 3, 0, 0,
tile_set = ExtResource("2_iov41")
use_kinematic_bodies = true

Step 3: Check the box for "use_kinematic_bodies = true", save file

Step 3 Results:

There are two identical lines in the .tscn file, one of which doesn't show up in the Editor

$ grep -rni use_kinematic_bodies .
./moving_platform.tscn:11:use_kinematic_bodies = true
./moving_platform.tscn:17:use_kinematic_bodies = true

### Minimal reproduction project (MRP)

[repro_error.zip](https://github.com/user-attachments/files/20509020/repro_error.zip)