Since the equipment under test is being powered via an isolation
transformer you should ground the scope probe ground to the negative
side in the hot chassis in order to obtain proper waveform
measurements.... no problem, no sparks, not an issue.
Obviously voltage and current are still present and standard personal
safety proceedures are still required, but because the scope is safeyy
grounded there are not hot chassis issues since they are floating
thanks to the isolation transformer.
electricitym