Just for clarification:
The old SLOs used the following topology:
Preamp gain stages (3 for Lead, 2 for Normal)
Gainstage + DC coupled cathode follower into FX send (send buffer)
Gainstage + DC coupled chathode follower into tone stack (return recovery stage + tone stack "buffer")
Tone Stack
Master Volumes
Phase Inverter
Power Stage
-> FX loop including its two tubes is part of the signal path.
The new SLO supposedly has the following topology (at least accoridung to the fine folks at SLO clone forum, the schematic posted there may or may not have errors):
Preamp gain stages (3 for Lead, 2 for Normal)
Gainstage + DC coupled chathode follower into tone stack (tone stack "buffer")
Tone Stack
Master Volumes
AC coupled cathode follower into FX send (send buffer)
Gainstage (return recovery)
FX volume
Phase Inverter
Power Stage
-> FX loop including FX volume pot is switched in or out
My concern with designing a loop like this, and this is particularly true when you would want to use the loop's "footswitch-ability", the signal levels around the loop are highly dependent from where you set your master volumes.
Like I described above, the master volumes are essentially your send level pots, when the loop is engaged, and the FX level pot at the back of the amp acts as your actual master volume.
What's perplexing is, that Deadpan hears a small volume increase when adding a patch cable and loop engaged. Because with or without cable the signal path should be literally the same, and so should volume.
I think, without modding the amp, you might need to get along with the behaviour, assuming everything is working properly with that loop. I mean, an ever so small tone alteration with the loop on, I'd say, can be expected, even without driving them into saturation, since we have two tube stages added in and out of the signal path. This wasn't the case with the old SLO.
If you experience your best sound with loop level at max, I assume, you would use the channel master volumes to control you actual playing volume. I'd expect you won't be able to turn up the masters so high that the FX unit or the two tube stages would really distort, without severely hurting yourself.