I can tell you why this is happening! I think!
OK, so first off, FKMS vs KMS.
KMS is Kernel Mode Setting. This is the kernel's framework for setting video modes, abstracting over HDMI/DSI initialization, timing parameters, etc. etc. across platforms.
FKMS is still KMS, but it's a special KMS driver for the Pi which sets up HDMI using the DispmanX API into the Broadcom proprietary OS that runs alongside Linux on the Raspberry Pi. This is nice because it's dead simple for Linux (Linux quite literally gets to say "yo, gimme a 1920x1080 layer!") but bad because it relies on a proprietary blob and the blob can't be extended.
Native KMS, on the other hand, sets up HDMI using native device access to the actual registers which affect the HDMI encoder, DSI link, and so on. This is more extensible and isn't closed source, but it's also mega complicated.
Now, here's the kicker on your Pi. Other commenters are correct that normally, KMS should just affect mode setting, not rendering. But, on the Pi, this isn't true. KMS and FKMS _also_ affect the way _layers_ are configured in the DRM (Direct Render Manager) subsystem.
Why? DispmanX isn't just a mode setter, it's also a scaling and compositing (layering) engine!
So, in the course of bypassing DispmanX, the DRM system in KMS mode now needs to act differently - it needs to configure 2D compositing planes through the KMS system instead of through DispmanX.
What's on a separate 2D compositing layer?
The legacy cursor.
Here's the switch where RealKMS is responsible for setting up the cursor compositing layers, a task which in FakeKMS was already handled by DispmanX:
https://github.com/raspberrypi/linux/blob/aeaa2460db088fb2c9...
https://github.com/raspberrypi/linux/blob/1fe617a917eac75800...
Now, _why_ this makes your cursor lag, I don't know, but that's the difference.