One more follow up lol. So after some more experimenting I found the same stutter in Watch Dogs Legion, which led me to believe that something either must be going with Ubisoft Connect or some other program. Turns out I was right. So I usually cap my framerate with RTSS as seen in the video. However for some reason, the RTSS cap feature is causing stuttering on ubisoft connect games when using a PlayStation controller, not the overlay itself, just the cap feature. When using the framerate cap from Nvidia's control panel, the stuttering is totally gone. Very odd.

Further follow up, managed to fix the stuttering by adding AC Valhalla as a non-steam game, and using steam's controller config to make the game think it's an Xbox controller. So that resolves my issue, however it would be nice to able to use the haptic feedback.

@chawliethefair
As a follow up, I have also tried several different USB ports, ones both on my pc and from a powered usb hub, all give the same results. xbox controller has no stuttering, playstation controllers do.

So on the PC Version of the game there appears to be a heavy constant stutter when using Playstation controllers, both Dualsense and Dualshock 4. With an Xbox Controller there is no stutter.
I tested a DualSense, a DualShock 4, and an Xbox Series controller. All three were wired via USB. I also tested the hybrid, mouse, and controller only options, none of these had an effect. I also tried controller vibration on and off, this also had no effect. I also made sure Steam wasn't running during these tests, and made sure to disable the controller speakers and/or microphones through the windows control panel. As long as a PlayStation controller is plugged in, even if in the game options the "keyboard only" mode is selected, the game stutters. Unplugging the playstation controller immediately fixes the stutter. Now this may be a Windows 10 problem, but I'm unable to replicate this behavior in other games.

My Specs:
RTX 2060 Super
Driver Version 471.11
Ryzen 3700x
16 GB Ram
Windows 10 Pro 64 bit Ver 21H1

Here's a video of the issue with an FPS counter, I try all three controllers in the video: