When it comes to the isolated probing, each method has it's advantages and trade offs, click
HERE and download the Tektronix "
Fundamental of Floating Measurements and Isolated Input Oscilloscopes".
Imo the best but the most expensive method
is to use an isolated scope, still it has it's trade offs
. But you can use each scope's channel as in your case since each channels are isolated each other.
Example illustration from Tektronix isolated scope design.
Example what you can do with an isolated scope, watch the different hook points at both probes ground clips, you just can't do this with ordinary scope, even using an isolated transformer or floated scope/dut.