It's way too early to say, but if at all possible, I'd assume using built in routines.
We don't need another unmanageable asm only, hard coded to the hardware mess.
For all you know, the machine it runs on may not even have the custom chipset.
Once it does work though, I'm sure it will fork all over the place.
There will surely be 1.3-type ROMS for old games, 3.1-type, 060 specific, ROMs for super-expanded Amigas that boot directly to RTG cards with USB input, etc.
Aros will really open up a lot of options without needing OS3.1, Picasso96 or CybergraphX once it's finally complete.