Nope. GM9 won't run .bin files. But it will run converted payloads -- Gateway, AGBSave9, and EmuNAND9 (no luck with Puma) run just fine. Just copy the .firm files you want to run to the "gm9/payloads" folder and they'll show up on the "Payloads" menu. BootCTR9 seems to run .bin payloads just fine, though (will even run Puma). Actually, even CBM9 can run AGBSave9 and EmuNAND9. Luma's chainloader is just garbage. It can't even run Cakes until you launch it with BootCTR9 or CBM9 first (I tried making my CakesLauncher script an SSR, and it still wasn't enough).
I think you mean 1.2 (aka that attempt by the Luma team to pull a "GW Fastboot" and cut everyone else out of the picture). 1.3 broke nothing. Actually the example given by the firmtool readme still works (I would add "-i" for good measure -- screen init). Here's the thing. They work in BootCTR9 and GM9. The text mode ones even work in CBM9. Luma's chainloader is the only thing that chokes on these, so I think it's the problem. Why use it? Just use BootCTR9. It's always been the best chainloader hands down. Or replace B9S with GM9 and have a good chainloader built right into your firm (if d0k3 ever adds hotkeys, there will be no need to have boot.firm include a chainloader at all). Besides, scripts menu at boot, FTW