I think -
think - the main purpose of the smart charging unit is to take the alternator out of the loop so it drags the engine less, and it only enables the alternator when it's less likely to use fuel (ie it'll make it charge off throttle or during light braking, rather than on a steady throttle etc) or when it's badly needed (in the rain, at night, with lots of accessories on, etc).
Believe it's one of the reason the bigger engined cars like the x35i/x40i can do ~40mpg on a run in eco mode - less mechanical drag on the engine (it also uses the AC a lot less in Eco mode)
I'm not 100% on whether running without that and constantly charging would cause the ECM to throw a fit if the battery is constantly at 14v, though (it might expect it to float between 12-14 and consider constant 14v to be a fault) or whether constantly charging an AGM might impact it's lifespan, although I don't
think it would. With that said, bear in mind that the alternator on the F20 135i/N55 is rated for over 200amp, and the E46 330 is ~120amp so it'll be throwing a fair bit more current in, which might be of concern?
If it's not throwing codes, I'd risk it for a biscuit - but maybe not use it for any long runs/as a daily till the part is replaced. You'd
assume the failure mode of 'don't charge the battery' is there for a reason, but it genuinely could just be a shockingly bad design choice given that, as you've learned, it just lets the battery run flat without much warning
