Just to cap off what was stated... Since the 5BEQ is positioned before the loop, the attenuation of the signal occurs in the 5BEQ circuit for the FX loop or is bypassed to the PI if the loop is turned off. Mind you the send level will by taken out of the signal path in hard bypass. Even with the 5BEQ turned off, the signal still passes through the emitter follower transistor circuit, summing amp and final output transistor which is a PNP driven by the summing amplifier (or differential circuit). There is no hard bypass around the 5BEQ. This circuit will effect the tone of the amp to some degree and usually becomes boosted with the 5BEQ turned on as the differential amp is effected by the tuned circuits for the EQ. I doubt that this circuit is any reason for concern as it does the same thing the others do just with different components.
Many other factors dictate the overall tone of each amp, most of which is in the power supply and the voltages applied to each preamp tube. Perhaps one way to determine any differences is to slave the FX loop send to a return of another amp. I may actually try this just to hear what differences the preamp of each compares to each other. I have done this with the Mark V slaved into the Roadster already since I was trying to figure out if it was the bias on the power tubes or the preamp causing the ice pick tone. It was the preamp circuit as the Roadster definitely had the ice when slaved by the Mark V. (yeah the output level may be a bit too high for an instrument level loop of the Roadster but I was able to rule out the power section of the V causing the ICE).
Many other factors dictate the overall tone of each amp, most of which is in the power supply and the voltages applied to each preamp tube. Perhaps one way to determine any differences is to slave the FX loop send to a return of another amp. I may actually try this just to hear what differences the preamp of each compares to each other. I have done this with the Mark V slaved into the Roadster already since I was trying to figure out if it was the bias on the power tubes or the preamp causing the ice pick tone. It was the preamp circuit as the Roadster definitely had the ice when slaved by the Mark V. (yeah the output level may be a bit too high for an instrument level loop of the Roadster but I was able to rule out the power section of the V causing the ICE).