Single ended scope probes on equipment under test which ARE on an isolation transformer
With the majority of oscilloscopes, the ground of the input channels is connected to the AC supply ground pin.
If you connect the probe to a signal that is not referenced to ground you risk getting a contaminated signal or worse causing damage to the device under test or the oscilloscope. With both of your examples you will be shorting out either the LLC isolation or the isolation transformer in the alternate set-up.
If you only use a single channel at a time then some of the arrangements may be usable, but if you are using two channels the probe grounds could for example short the PFC and the amplifier even if the scope is on an isolation transformer.
You could power the oscilloscope from an isolation transformer or use a battery powered scope.
I have occasionally lifted the ground on the power lead of the scope to perform successful measurements but that is potentially dangerous as the front panel controls on the scope could be at dangerous voltages.
The best approach is to use an oscilloscope with isolated input channels designed for such situations such as the Tektronix TPS2024B.  Each channel is isolated from the power ground and from each other.
It simplifies the problem greatly if you only look at one side at a time.
However, one non-obvious issue with modern power supplies is that commonly there is a bridge rectifier at the input followed by the PFC; all parts of the PFC will be 'live' as the bridge diodes will be alternately connecting the positive output to one side of the incoming AC line then the other and the same for negative output.
The circuit can be safely probed if fed from an isolated AC supply as you have you. When the ground of the scope is connected these voltages will be forced on the incoming AC. you need to always be aware that even the neutral side of the incoming power to the PFC is live.