"Store transformation" is not very accessible buried inside the properties dialog.
There should be some accessible way to change it and also a way to apply a matrix to the shape in an "optimized" way.
Using path operations as a hack to reset matrix explode primitives like rectangle or circles to generic paths.

I'm I missing something or is this feature absent?
I guess it should be very simple to implement. A scaled circle in "optimized" mode is still a circle so the functionality is already there.

One of the oldest "bug" of inkscape is managing transformations. Like even the coordinate system is flipped from the specs and there is no way for a proper fix -as far as I know by solving it on new documents would make opening old ones "broken".

Yes, that is a requested feature, I'm sure it has a bug report in the bug tracker.

There exists an extension that will apply all transformations: https://github.com/Klowner/inkscape-applytransforms (just in case this helps anyone - it's obviously the opposite of what you're asking for, rsf...)