I'll try to explain this in a way that should clear up the confusion.
In all systems MTS, the initial gain stage is always in the amp itself. The modules contain the 2nd through 5th stages and use as many as the need in a configuration of signal flow that is most traditional to the given circuit being emulated. For example, a Fender clean preamp like a stock Blackface would flow through the amps initial stage, plate coupled to the EQ, into a makeup gain stage and out through a cathode follower (not a traditional decision, but not all that significant either). A stock Plexi module would flow through the amps initial stage, through two more gain stages (again, a Plexi would have only had one here, but that's also why a stock Plexi can have more gain than the real deal. Trade offs for system flexibility) and then feed the EQ through a cathode follower.
Because gain stages in series are exponential regarding signal growth, the initial stage has a very significant influence on everything after it. The original Randall and Egnater MTS amps had a traditional Fender stage up front made up of a 100K plate resistor, 1K5 cathode resistor and a 22uF bypass cap. This provides a nearly full-frequency amplification (35.46dB) from 100hZ up, which covers almost all of the guitars relevant frequency range. A low E is 82Hz and the roll off is only 0.05dB down from 100Hz to 82Hz. Think of this as biasing the preamp tube stage.
The other two variations provided via the Synergy modules and hardware are a 2K7/0.68uF (traditional in a Marshall or Friedman) or a 1K8/1uF (traditional in a Soldano, Mesa Rectifier and Peavey 5150). The 2K7/0.68uF stage provides 35.45dB of amplification gain from about 1500hZ and up and rolls off to 28.88dB at 82Hz. The 1K8/1uF stage provides 35.45dB of amplification gain from about 1000hZ and up and 30.64dB at 82hZ. Similar to the Marshall-style selection, just a touch thicker sounding. The Fender-style selection of 1K5/22uF will be perceived as louder and thicker sounding by a good bit.
When modding modules, we always had to compensate for the first stage that we can not change at the module level. Various things were done like changing the initial coupling cap (the "C3" mods or switches documented here) or various other tuning decisions. The Tight/Bright switches on the Egnater dual channel modules provided variety stock in this respect. Various switches on modified modules added other options. When installing the JFM Input PCB, I often ask if there is a preference and build the front end accordingly. Dave Friedman typically changes it to a traditional Marshall stage on the MTS amps he has modified.
What is cool about the Synergy circuit is the ability to try three options at the stock module level. Just because something is "traditional" doesn't make it best for each player and situation.
Hope this helps clear some confusion up.
