Recently started noticing a lag with my Magic Mouse 2 when my 2020 16" MBP is utilizing my RX560 eGPU. I have tried adjusting the resultion on the 2 attached monitors to no avail. I have also reset the SMC and the NVRAM. No change.
Might not help but I had interference on my Mac mini with Bluetooth mouse / keyboard when certain things were plugged in (that said it was USB 3 rather than thunderbolt), changing ports helped it as did subsequently using an adapter but it’s not an ideal solution.