Or Thunderbird is much older and has a lot more users

Blender is actually much, much older than Thunderbird.

wow, did not expect blender to be 32 years old, thanks for correcting me.

but still, they were open sourced about 1 year apart. I still think having a bigger user base is a good reason for the difference

That's relevant to why it historically had bizarre UX issues, like ctrl+s being the shortcut to erase the scene and start a new one: it predated most of those conventions, and has its own UI tooling. It's also always been designed to use three mouse buttons, coming from the Unix world, which used to be problematic when not everyone had a mouse with a clicky scroll wheel.

It's come an absurdly long way since I first dabbled with it in the early 2000s, and has gone from a niche FOSS tool to something widely used in its field.

Nowadays, Blender is an example of masterful UX for a professional tool. Immediately responsive, information dense UI with keyboard shortcuts for absolutely everything. Actions are composable, like with vim: something like "ex5" will extrude five units on the x axis.

UI standardization, CUA, X11, Motif date from the late 80s.

Right, but those are for simple tasks. Much like vi or emacs, the keybindings are esoteric and historical but so much of what makes the tools great is reliant on on said historical and esoteric behaviour that changing any of it becomes an exercises in futility