To me it seems like the 0 watt amp thing in Synergy modules is just marketing speak for them building a Post Phase Inverter Master Volume circuit into a module, which I mean is really cool, but that's what it is. Basically it's a power section without power tubes. It's kinda confusing though because a 12AX7 can put out about 1 watt of power which is loud as shit compared to standard line level, which is where these modules are supposed to be operating. Still, imo it's a necessary component for being able to get the sound of a non master volume amp in a module, as the phase inverter breaking up really is the majority of where the distortion comes from in those vintage amps.
I don't see doubling up on phase inverters in a Synergy system to be all that much of an issue though, as I'd imagine most people are going to run the real poweramp in a Synergy system fairly clean so the "real" phase inverter isn't really going to influence the sound to any real non-linear degree. If you're running a single module into a tube power section that's breaking up though, yeah that will impact things but I wouldn't think that's the way most people are running these setups.
As far as the Class D amp claims, I can't imagine a Class D amp sounding "just like" a real tube poweramp, unless under the most curated and specific conditions, so like both amps would need to be working quiet enough that they're not clipping at all, and the Class D's DSP chip has an EQ in it to emulate the impedance curve of the exact cab and tube poweramp pair being compared or something. But even then, it's only going to mostly work with that one cab and tube poweramp the Class D's DSP chip has been matched against. Mismatch the real poweramp or the EQ signature the DSP is applying to match the impedance curve of the specific cab being used and all bets are off.