Describe the bug
When using Apply Chosen Modifiers on a rigged mesh, the armature's pose is applied to all shape keys (except for the basis) even if the Armature modifier itself wasn't selected.
To Reproduce
Using a rigged mesh:
- Add a modifier and some shape keys
- Pose the armature
- Apply all modifiers except Armature
- Basis remains as expected, but all other shape keys now have the pose baked into them
Expected behavior
The resulting shape keys should not be affected by the armature's pose as the Armature modifier was not selected to be applied.
Screenshots
Initial pose:

Before applying:

After applying mirror & subsurf:

Desktop:
- Blender Version: 4.5.2
- OS: Windows 10
- SKkeeper Version: 1.8.2
Additional context
Here is the model used: https://drive.google.com/file/d/1JweY-cPtiY4IDEEJwRxBbToD_itdHrZT/view?usp=sharing
This only includes the part of the model that is affected as well as part of the rig and two empty shape keys. Upon applying the mirror and subsurf modifiers here, the second shape key is modified despite both initially being the same.
In this case, I want to export with a different pose from the actual rest pose because I had issues with how the feet would animate when modeled against the ground like in the initial pose image where it bends unnaturally when straightened out, but still needed the exported pose to have the feet on the ground for VRChat.
This does not happen when the armature is set to its rest pose, so this should be fixable by simply checking if a mesh is rigged and setting its armature to rest before applying modifiers and restoring the armature state afterwards.
Describe the bug
When using Apply Chosen Modifiers on a rigged mesh, the armature's pose is applied to all shape keys (except for the basis) even if the Armature modifier itself wasn't selected.
To Reproduce
Using a rigged mesh:
Expected behavior
The resulting shape keys should not be affected by the armature's pose as the Armature modifier was not selected to be applied.
Screenshots

Initial pose:
Before applying:

After applying mirror & subsurf:

Desktop:
Additional context
Here is the model used: https://drive.google.com/file/d/1JweY-cPtiY4IDEEJwRxBbToD_itdHrZT/view?usp=sharing
This only includes the part of the model that is affected as well as part of the rig and two empty shape keys. Upon applying the mirror and subsurf modifiers here, the second shape key is modified despite both initially being the same.
In this case, I want to export with a different pose from the actual rest pose because I had issues with how the feet would animate when modeled against the ground like in the initial pose image where it bends unnaturally when straightened out, but still needed the exported pose to have the feet on the ground for VRChat.
This does not happen when the armature is set to its rest pose, so this should be fixable by simply checking if a mesh is rigged and setting its armature to rest before applying modifiers and restoring the armature state afterwards.