You are using the word gain incorrectly as most people do. Many think that distortion means high gain, it does not. Gain is an increase in something. Your guitar signal for instance, typically at around 640mV peak to peak that gest increased between each gain stage. If it did not, there would be too weak of a signal to drive the phase inverter and power tubes. I never measured the voltage amplitude on the circuit level on each gain stage. but did at the FX loop output.
Gain is to increase. Does not mean it gets distorted. Unfortunately, the FX send level drops the signal down to near instrument levels so they will be in the same range. The first image the signal increased from 640mV peak to peak to 1200 mV peak to peak. That is an increase. All gain stages increase the signal level, if not cut-off or clipped the amplitude will be higher thus have more gain (do not confuse the proper use of the word with distortion, so many people use the word gain improperly, confuse the "high gain" with distortion. Not to stir the pot here. I miss-use the term myself so it is common to say high gain, but in reality it is high distortion that then gets amplified or increased on level (also called gain but that usually takes place in the power section more so than the preamp). I knew that using the literal meaning of gain was going to piss off a few. Just use an open mind, nothing more.
Believe it or not, the circuits that create the distortion generally have the lowest gain factor, they are meant to be overdriven by the previous stage to force it into clipping or cut-off. It will be followed by another gain stage to boost the signal levels. Those are the facts. Once you clip or cut off the signal it will have a lower amplitude than the clean signal that is not distorted. Hence there is more gain on clean, just without the distortion many confuse as being high gain. This was measured from the JP2C clean channel. The green line is the output waveform from the FX send. Yellow curve is the input signal measured on the input. The scale on the input and output channels used on the scope were the same. All channel controls were set at noon. Sorry, this was from a larger image and also had the status field showing details that are hard to make out with this image. This had an input amplitude of 649mV peak to peak. The FX output level was 1200mV peak to peak. The gain here is 184% increase.
This is the same applied signal with no changes, Only changed to CH2. The input and output amplitudes are about the same, input still at 649mV peak to peak, distorted signal is only 770mV peak to peak. That is only 118% increase or gain from the original signal but highly distorted due to the overdrive circuit. The waveforms do contain some complex harmonics and will have a more compressed sound compared to the clean channel.
OK, sure there are two additional gain stages in the circuit on CH2 of the JP2C, that is the overdrive and booster stage. the overdrive distortions only half of the waveform, the booster stage cuts the other half. The top and bottom of the distorted waveform are not identical, they are different.
Sure, there may also be differences in the gain stages from one channel to the next. I am not going to dispute that. I am only taking a look from an engineering perspective. The JP2C is similar in design to the Mark VII but with obvious differences as it has a dual pot on the channel volumes. One is after the FX loop and the other is more or less in front of the FX loop. Different modes, regardless of channel will address the signal level in front of the V2A triode that is used to create the send level and different configurations on the recovery stage V2B. Some of that will address the OP's issue relating to use of a looper in the FX loop with captured content from the clean channel and played back using the other channels in a more distorted configuration (yes, I mean high gain channel as I have also adopted the incorrect use of the term).
As for the Mark V90, There will be differences in the output of the amp based on voice and channel selected. That holds true to other amps as well like the Dual Rectifier. It is all based on changes in the presence circuit, if the NFB is connected or bypassed. This all ties into the phase inverter circuit on the control grid side. The power section does not change as it is at a fixed bias. OK, if you change the power mode from 90W to 10W or whatever.
Another point, considering the Mark VII amp, say on CH3, The IIB mode bypasses the overdrive gain stage and sends the tone stack signal directly to the high gain stage I referenced as a booster stage. Well, IIB has less distortion than say IIC or IV modes that use the overdrive gain stage (has the lower gain factor but used to force the signal into the cut-off region). I do plan on scoping the different modes using the same method I did when looking at the dB levels of the FX loop of the JP2C, Mark V90 and TC50. Note that the TC clean had the highest output level at +8dBu compared to the CH2 (vintage lo) or CH3 (vintage high). The "high gain" channels did not exceed 3dBu if I remember correctly. Less gain but more distortion. This is all due to clipping and cut-off of the signal. Also the TC50 uses op-amps following the tube circuits so on paper that amp has the highest gain ever, does not mean much if the signal level does not increase as much as the circuit gain would indicate. If it did, it would sound like crap. I am not fond of hearing square wave signals as that is more of an ice pick in the making.