I would put the loop before the master volume. If it’s after the master, you will get bad signal-to noise ratio at low volumes and you’ll have to adjust the send level every time you change the master.
If it’s before, you get a fairly constant and predictable level going into the loop. The send level becomes set and forget (probably don’t even need a pot for it).
I started looking at JCM800 schematics for effects loops about 15 years ago when I just had finished building my JCM800, and the only two that I found *both* inserted the effects loop post master volume, which to me didn't make sense. A master volume is intended to push a hot signal into the power amp as to drive the pentodes into compression mode. Certainly not intended for effect pedals expecting an input signal from an instrument. Like you, I figured that if the effects loop was inserted before the master volume, one could take advantage of both the tone shaping of the effects pedal *and* driving that power amp to its edge.
But... since I rarely (and I mean rarely) use an effects loop, I'm not going to question the design and just build it with the designed/intended values. And for the very few times that I might use the effects loop, I'm just going to set the MV for the most neutral signal, and let the effect pedals color the sound. So most of the time (like almost always), the DPDT switch wil bypass the loop.
But that's the beauty in building your own amps: you can tweak, experiment, and reverse if not satisfied. So maybe one day I'll give it a shot. But for right now, just too happy with JCM800 tone that I currently have.