Hypothetically - what you're describing is exactly how BL is designed to work, as far as I know. Put it on a female, it drives thrusting from both atoms, aligns everything, runs female stim cycle with all the trimmings (voice, aheago, etc) and provides basic male 'load' and orgasm. Alt-futas don't need to be involved in that scenario at all, it should work perfectly fine. Your male's stim and orgasm won't sync to his VAMMoan though - he'll essentially have two stim cycles running for him, the one controlled by BL on the female, and the one controlled by his own VAMMoan. He'd cum twice at different times. So you'd have to pick one of two options - first would be to disable BL's male system entirely by unchecking everything and setting Stim Gain to 0, and use VAMMoan/REF to run everything independently on the male. Second would be to use the 'on male orgasm' trigger from BL to manually trigger orgasm in either REF, VAMMoan, or SexyFluids on the male (in whatever order/combo makes sense). But he won't moan in increasing intensity with the second setup, he'll just orgasm when BL triggers it. Thrusting and female stim/orgasm should work fine in both though.
However, If BL isn't recognizing the male atom's penis at all, I would disable REF altogether, give him an erection using simple morphs, and try that. If it works, it's a conflict with something on your male - either REF or something else. Try a bone-stock default male character - apparently certain skins can sometimes cause a gender detection issue, no idea why but I read that somewhere recently. Add the plugins back one at a time and see which one breaks it. You can also go into the Debug tab in FillMeUp and hit 'print registered penetrators' - that should show you if BL is even recognizing the male's penis in the blue message log in VAM (it certainly should). If REF is causing BL to not register the penis, that's a question for CheesyFX or our dear RunRudolph here. That's above my pay grade in terms of backend code stuff haha.
