The current firmware does indeed support either SD or HD, but the inputs only synchronize; they do not do standards conversion. The bottom line is that you must set the ATEM to whatever format you want the output to be, and then every input needs to conform to that format. This detail is given in the current revision of the manual (they updated it along with the software). The sort of mixed-format functionality you seem to be looking for is more expensive: you find it in something like the Ross Crossover, for example.
Another improvement with the newer firmware: you can map physical inputs to whichever switcher buttons you prefer (and the keyboard hot keys follow). If you use the GPI / Tally interface, its relays aren’t affected by the keyboard remapping: that means that a given relay always corresponds to a particular physical input to the switcher, which is nice: different users can customize the panel to their preferences without worrying about messing up camera tally.
Two issues I notice that are still unresolved: the switcher does not pass closed captions, and there is no provision to use the GPI inputs from the GPI / Tally adapter to control switcher functions.
— Jeff