Objects with both `__slots__` and `__dict__` have much larger size than needed (up to 4x) on Python 3.13

Bug report

Bug description:

On Python 3.13, instances that have both __slots__ and __dict__ defined (e.g. through inheritance)
can have a size that is more than four times of that in previous Python versions (e.g. 3.12).

import tracemalloc
import gc


class _Point2D:
    __slots__ = ("x", "y")


class Point3D_OnlySlots(_Point2D):
    __slots__ = ("z",)

    def __init__(self, x, y, z):
        self.x, self.y, self.z = x, y, z


class Point3D_DictAndSlots(_Point2D):
    def __init__(self, x, y, z):
        self.x, self.y, self.z = x, y, z


class Point3D_OnlyDict:
    def __init__(self, x, y, z):
        self.x, self.y, self.z = x, y, z


gc.collect()  # clear freelists
tracemalloc.start()
_ = [Point3D_OnlySlots(1, 2, 3) for _ in range(1_000_000)]
print(
    f"1M Point3D (only __slots__) instances:         {tracemalloc.get_traced_memory()[0]:_} bytes"
)

gc.collect()  # clear freelists
tracemalloc.start()
_ = [Point3D_OnlyDict(1, 2, 3) for _ in range(1_000_000)]
print(
    f"1M Point3D (only __dict__) instances:          {tracemalloc.get_traced_memory()[0]:_} bytes"
)

gc.collect()  # clear freelists
tracemalloc.start()
_ = [Point3D_DictAndSlots(1, 2, 3) for _ in range(1_000_000)]
print(
    f"1M Point3D (__dict__ and __slots__) instances: {tracemalloc.get_traced_memory()[0]:_} bytes"
)

On python 3.13.3, this prints:

1M Point3D (only __slots__) instances:         64_448_792 bytes
1M Point3D (only __dict__) instances:          104_451_928 bytes
1M Point3D (__dict__ and __slots__) instances: 416_448_848 bytes

On python 3.12.11, this prints:

1M Point3D (only __slots__) instances:         64_448_792 bytes
1M Point3D (only __dict__) instances:          96_451_808 bytes
1M Point3D (__dict__ and __slots__) instances: 96_452_232 bytes

The apparent cause seems to be the object layout changes (see here)
which introduced inline values. It appears that these don't mesh well with __slots__.
Could this be because the inline values need to have a fixed offset?
What appears to cause the dramatic increase above is that having (nonempty) __slots__ will
trigger __dict__ materialization (size 30) as soon as a non-slot attribute is set. In contrast to the optimized "no slots" case, this dict doesn't shrink as more instances are created.

Of course, mixing __slots__ and __dict__ is not recommended, but it's a trap that can be easily fallen into.
For example, if forgetting to define __slots__ anywhere in a complex class hierarchy.

I'm unsure if I'm understanding exactly what's going on though. @markshannon perhaps you can shed some light on this?

Related: #115776, #115822

CPython versions tested on:

3.13

Operating systems tested on:

macOS

Linked PRs

• gh-135389
• gh-156656

Start with the object layout changes described in Objects/object_layout.md and reproduce the issue using the supplied slots/dict classes with tracemalloc on Python 3.13 and 3.12. Review linked PRs gh-135389 and gh-156656, then verify that mixed slots-and-dict instances no longer incur the reported excess memory while preserving the demonstrated layouts.