I think I've found the "solution".

I think I misunderstood the source of the issue (I was blaming Clip studio). But having done a lot more testing in both krita, sai and photoshop, the same issue more or less pops up there.

The issue isn't that the canvas is being drawn at a lower framerate, it's that my tablet (intuos 3, pretty old one) only has a polling rate of 125hz. Being used to a 1000hz mouse, the difference between responsiveness is extreme.

There's also the calculations the computer does in regards to tablet input (pressure sensitivity, tilt, triangulation calculations), which is very different from the much more simple input it gets from mice. This also has an impact on how many times the input gets updated on the screen. These two phenomena result in this issue I blamed on FPS lag in my OP. If I move the cursor side to side or in circles with my mouse, the "ghosting" that the cursor does is smooth. If I do the same with my stylus on my tablet, I notice gaps in the ghosting trail (as if the operating system hid the cursor for a frame or two).

Basically the solution is that there is no solution (at least not software-wise), and that the problem isn't really that big of a deal. It can probably be remedied a little by getting a newer tablet (mine is from 2008, some newer ones have a polling rate closer to 300hz). But again this isn't a huge issue so I'll just get used to it. I hadn't really drawn much since I went from using a 100hz monitor to a 165hz one, which is why I notice this issue more than in the past.