Steam Deck has better software support than ROG Ally. Also, the latter only sports standard analogs, and SD offers two trackpads (which are great, btw).
On the other hand, ROG has more raw power and a better display. I don’t know anything meaningful about the rest you mentioned.
As for the OS, Linux seems better suited for these kinds of devices. Proton runs almost anything and offers a great experience, and on top off that, you can still use it as a daily PC with the use of peripherals. But I’m probably somewhat biased, as I know and love my SD.