Well, at this point you have ruled out apps, drivers, services, clean install, clean boot, GPU audio, and input rate, and perhaps it reproduces only on Windows 11 and not on Windows 10.
The best next step is to get this in front of the Windows graphics team with a Feedback Hub capture and the traces you already recorded.
Open Feedback Hub from Start and choose Report a problem. Give it a short title like Choppy window drag or scroll for a few seconds on dual 144 Hz monitors. Pick the category Display and Graphics then Desktop Window Manager or Windowing if offered.
Now turn on Recreate my problem, start the capture, and use the PC normally. It is fine if the issue takes several minutes to appear. When you have felt the choppy motion for a few seconds, stop the capture and submit.
Before you submit, attach the three .etl traces you created with WPR and your LatencyMon text. Also attach a DxDiag so engineers get exact device and driver info. To create it, press Win+R, type dxdiag, press Enter, click Save All Information, and attach the dxdiag.txt file to the feedback.
In the description, include these facts in one paragraph so triage has full context:
Windows 11 shows brief choppy motion while dragging or scrolling on two 144 Hz Asus monitors. Windows 10 on the same hardware does not show it. Clean install and clean boot still show it. HAGS, VRR, Optimizations for windowed games, Game Bar and background capture are off. MPO was tested off with OverlayTestMode=5. Nvidia audio was disabled for testing. GPU is MSI RTX 4070 Gaming X Trio. Monitors are VG27AQL3A 1440p 144 Hz and VG278Q 1080p 144 Hz.
Once that is submitted, the Windows graphics team can correlate your live capture with your ETL traces and driver stack to isolate the regression. This is the most direct route to a permanent fix.