I think a lot of people come around to the physical BE through the gateway Axe-FX version. I certainly did.Not sure if this is the best place to ask this.
After using the Axe FX 2 for a few years I have basically decided that the amp tones I like are the BE-100, Bogner Ecstasy, and Dirty Shirly, .
I know from years of fist fighting Mesa Boogie amps that I simply do not like the tonal coloration of 6L6 tubes. I am, as you would say, an EL34 guy, and the prospect of running a pre-amp designed for EL34 (BE100) into 6L6 tubes seems like a recipe for disappointment.
Dunno, need advice.
This subject comes up a lot- personally, I think it is way overblown. I think that you might really prefer an EL34 amp over a 6L6 amp but I don't really think it is the tube type themselves. I don't know which Mesa amps or what all you've done to fight them but usually the preamp topology is a lot different than a typical EL34 amp, so I would expect the result would be a lot different.
If I'm not mistaken, Dave Friedman has said in various videos that you can get the same sounds on an EL34 or 6L6 tube in the same amp just by adjusting the amp. I think I pretty much believe him, even though I don't want to believe him. I think the BE has EL34s because people really want it to have EL34's, not because Dave thinks they need to be there.
Dirty Shirley is 5881s, not EL34s. That's very similar to a 6L6 but its got very little else in common with the Boogie. Dirty Shirley is an early-Marshall kind of amp. Its not like a Fender at all. If you like that amp, maybe there is hope for you on non-EL34 setups. I think Cliff @ Fractal has also recently commented about the differences in power tube tone being more about the rest of the circuit than about the tubes themselves.
The modules will sound "different" in different poweramps. Whether a particular one will work for you is unknowable without trying it. I think they are better with a tube poweramp, despite being servicable without them. If you still have your Fractal, you have a million options inside it for that particular project.
The speaker cabinet should be the biggest factor by miles and miles. I've played Marshally modules through my Syn-30 (6L6) as well as Voxy type modules and a Fendery module. I don't know if they sound exactly like the real amps- probably not. They sound great though.
If they really needed to have an EL34 head and a 6L6 head for these to work well, I think Egnater, Randall and now Synergy would have done that. The modules generally work pretty well despite sharing a common poweramp.