The trouble with pass-though earth on an isol transformer, is that you can then only hook your scopeprobe ground to that node to which the pass through earth connects, on the secondary side of the isol transformer. If you do cut the pass-through earth, then putting a 1MEG resistor between isol txformer sec side "neutral" and earth is a good idea.
The problem with isolation transformers is that with BCM Flyback PFC stages at the front end, the isolation transformer leakage will ring with the input filter, so you cant use isol transformer with them.
The problem with diff probes , eg TA041, is that you get dreadfully noisy scope shots when you probe eg low value sense resistors.
If you know exactly what you are doing, you can float the scope (cut off the earth), and use it like that, but be very careful, dont touch anything metal on the scope when you do it......turn off the mains when you move the probe onto the circuit....ensure eveything is discharged....when you float it, you can then use eg a home brew coaxial probe to cleanly scope sense resistors on the primary side of the SMPS.......and get much less noise on your scope shot.