That looks OK.
I think you may be located in the US. If so, there are some differences between our power systems.
Outside the US, most power systems use what is called a 'Multiple Earthed Neutral'.
The 3 phase power system has a star connected secondary of 230 Volt per phase, and the star point is connected to ground at the substation. Each subscribers gets one, two or three phases plus a Neutral. At each subscribers switchboard, the neutral is connected to ground. Where you have a SMPS, the full wave rectifier produces a DC output which is NOT tied to ground anywhere; it floats above ground AND the power mains. So to measure waveforms in this type of equipment, you need a CRO which is also floating above ground. This is hard to do, so the best bet is to isolate the SMPS from the mains ground by means of an isolating transformer. Then the earth lead of the CRO test probe CRO can be connected to the DC common.
In the US, the power supply is supplied as a two phase (220 volt centre tapped) arrangement from the distribution supply transformer and my understanding is that the AC supply is not earthed anywhere.
I think your pics in post 4 are due to you have mains borne signals included with the input from the PCB.
You dont say what you did to get a sensible looking CRO display.
The display seems OK. Remember you have the MOSFETS disconnected (I think you said) so what the actual duty cycle should be, is not clear. Some of these switch mode IC's have a minimum (or maximum) duty cycle. If you have the mosfets disconnected, then there is probably no feedback from the voltage/current monitoring part of the power supply, so what you get may not have much relevance; except that it appears to be working. So now go to the next step.