Thank you! That was an good idea! I disabled the Turbo boost and confirmed first the clock would stay fixed at 3.5Ghz. Interestingly it did had an effect in HL:Alyx, the problem got worse, confirming CPU speed was at least a factor. I then proceeded the opposite way and overclocked the i7-4770K (since I already had installed a very strong cooler), and the studdering problem diminished - but was still present.
Over the week-end, I got my hands on a GTX1660 and swap out the RTX2070 for the GTX. I was hoping this would work - but it didn't. Maybe the root cause is deeper.. but who knows.
Nonetheless, I also received the new parts and now I have an Asus Z390-E Gaming with an i5-9600k. With the RTX2070, the issue has fully disappeared! HL:Alyx with HTC Vive Wireless is very sharp and fluid - everything at ULTRA!
I spent a lot of time trying to interpret the Bottleneck calculator of pc-builds.com, since they make interesting claims on matching different generations of hardware. I could not confirm their math (the community seems to have quite on debate on it to say the least) but in a way - I can see the logic behind it.
One piece of hardware can consume so much bandwith that in theory could make other pieces wait longer. If it were back in the 90s I would check the IRQ conflicts - but that is from a time long past. To solve this, I think a performance monitor tool of PCIe Lanes would be the next step - but I've never seen any such tools. More research would be key here.
Anyway - Thanks a lot for responding, since my new machine does not have the issue, i'll be enjoying the game for a while, rather than troubleshooting.
Thanks!