Any properly wired Variac should not upset a decent GFCI breaker.....
now, turning it on/off with a power switch MAY trigger the GFCI, my electric shaver does that to the GFCI breaker in the bathroom, it is one of two on the same circuit but only the one with the shaver goes off when shaver is turned off...just reset the GFCI, and hell with it....
Obviously referring to the main power switch on the Variac.....now as to load, I dunno, not messed with that configuration.....I would be more tempted to put the GFCI on the output....but that depends on your use, and why you need either one.....