This is true, there are two sets of Manipulator mapping for Ragdoll that depend on the two default keymaps.
BlenderkeymapIndustry Compatiblekeymaps
Where Blender uses the middle-mouse for navigation and Industry Compatible uses the Alt-key.
The graphics in the Ragdoll Manipulator only reflects those active when using the Industry Compatible keymap. Your best bet is hiding the help from the viewport and instead relying on the keys here:
If you’ve modified the keys beyond defaults, then the Ragdoll Manipulator view will not reflect this as of yet.
That’s interesting, we haven’t experimented with remapping keys outside of the Manipulator itself. I can’t quite wrap my head around how that would work though, since the Manipulator from Blender’s perspective is just 1 tool that intercepts all keys…
If you are tech-savvy, then the Python source is available here which is the same as in your installation directory.
There’s an especially interesting call here, which handles the remapping ahead of being passed into Ragdoll Core (as of release 2024.06.30).
If you make a change to this, then upon restarting Blender you’d see this reflected in your session.
And if you do find a workable solution, feel free to post it here and I’ll see if we can include this in the next public release.