I guess it does make to be careful with the Super NT (and other non-standard consoles) at this point because it may have its own flaws which may introduce additional complexity (which can be avoided at this point).
After the standard consoles (as reference devices) work well then it does make sense to adapt the code for non-standard consoles.
I've been testing the Super NT on firmware version 4.5, with the GSU firmware, and I've tested Star Fox 2, Star Fox, and Yoshi's Island, all NTSC ROMs.
All of them play with absolute perfection, but I haven't used version 7 yet, but version 5, as 5 has been super stable, never encountered a single crash or otherwise system error when running on an SD2SNES. I will test version 7 later, but AFAIK, it's amazing.