This is my run. I'm not seeing those CPU fluctuations at all....tx. That CPU fluctuation is normal for 16-core AM4 (my 5950X does that also). It's when they're left on auto and the 3950X will boost past 4750 until it gets reigned in by the GHz police. Below is the same default GPU setting as before but with the 3950X on all-core 4400; that's all this little AIO can take....nice and smooth ...once CPU and GPU are properly water-cooled, it's time to push this setup more.
...on the 6900XT w/ MPT 330W/350A, definitely voltage readout and may be voltage control are behaving a bit weirdly - is that normal after MPT changes ? I'm wondering if it relates to the Giga 3x8 pin arrangement and a VRM that's different from the reference card
...at the end of the day, the clock differences will not be noticeable in every-day apps. That said, what gives me pause is the huge delta between overall GPU temp and Hotspot temp you're seeing. On my card, the delta is rarely more than 20 C, often less.
...I've had four new IDENTICAL GPUs before purchased at the same time (incl. for workstations) and when taking them apart for w-cooling, some of them had some serious TIM imprint issues, others had a slightly crooked mount of the cooler, and/or some select loose screws. I realize that taking apart a brand-new (and hard-to-replace) 6900XT is not high on your agenda re. warranty etc., but have you considered emailing the EU HQ of your vendor and ask if you can re-paste / re-pad, given the issues you're seeing ? I've done that before and as long as you're straight-up with them ("no, I have no idea how the flux and shunt mods got on there") they tend to be helpful more often than not.
With Covid-19 impacts, IMO, I see more quality issues in various assembled computer components