But won't the Scope GFCI at least protect you and potentially the scope in case of the following "ground loop"?
Secondary hot -> Scope Ground -> Earth Ground -> "Human" -> Secondary Neutral.
Since GFCI's (at least in the US) also trip if there is a ground current (even if the hot and neutral currents are balanced), this fault should trip the scope GFCI protecting you and hopefully also the scope.
No, at least here in Germany these things trip on unbalanced live/neutral only. This is usually the case if there's an unintended path from live or neutral (or somewhere in between) to earth. That unintended path could be anywhere. From your description, your GFCI also monitors the current in the earth (safety ground) wire and will trip if this isn't zero. I haven't seen such a thing yet, according to I haven't seen any typical GFCI from North America except for some Electroboom (and similar) videos, such a thing may exist and even be in use at your place. I've seen some datasheets and app notes from typical GFCI controller ICs for the American market, monitoring the earth wire wasn't mentioned there.
So, in case the GFCI monitors the earth wire, it'll trip if your fault current diverts into the monitored ground wire, I agree. Typically a fault current through your body, aka electrical shock, won't divert into that particular monitored wire but somewhere else to earth. So this will be detected by non-balanced neutral/line only.
If you close the fault loop as ("Secondary hot -> Scope Ground -> Earth Ground -> "Human" -> Secondary Neutral") you said, yes a GFCI as you describe should trip. Anyway, don't rely on such thoughts, the fault will find another path to shock you without the GFCI tripping, that's for sure.
So, I just don't like this belts and suspenders approach at all, since it never covers all faults, just an increasing amount of faults that someone thought of while doing the fault analysis at an ever increasing amount of equipment, regulations and cost. But there will be always more faults that aren't caught. I prefer less belts and suspenders but rather using your brains, wariness and some simple rules (as "keep one hand in your pocket when messing around with dangerous voltages").
So, my revised question is whether the following is good belt & suspenders protection:
1. Mains -> GFCI#1 -> Scope
2. Mains -> Isolation Transformer -> DUT
That's the usual setup if you've got an GFCI employed. Everything is fine (as in normal lab practice) with that. Of course this setup can bear dangers to you, e.g. some elevated potential within the DUT that you might accidentally touch, and as it will be grounded at some point through the scope ground it is dangerous to you. If you're messing around with extra low voltage stuff, not a big deal, but be careful if you debug e.g. the primary side of an SMPS.
(of course, one shouldn't rely on GFCI's, circuit breakers, luck, etc for primary protection... but we all make mistakes and inadvertently touch things we shouldn't be touching
And if I get an isolation transformer with multiple outlets, this could also presumably help in the case of USB cables providing unexpected grounding connections so long as all the circuits are plugged into the isolation transformer.
USB ground loops are best dealt with USB isolators.