For body shop, RPC and really any other externally run mods, you'd just click the wine glass icon in Lutris and click "Run .exe in Wine prefix", same for simPE. That's the main reason I recommend Lutris. There might be some specific caveat to these mods, but I've used many external mods in other games this way without issue. Just yesterday I installed CheatEngine in my Ghost of Tsushima prefix to enable a mod which changes the parry timing indicator.

Re: SAI 2, in terminal:

xinput list

Find your touchscreen device e.g "HID-compliant touchscreen"

xinput disable "<HID-compliant touchscreen>"

This will disable touchscreen system-wide but is just to test and will revert upon rebooting. If it works, add an environment variable in Bottles:

WINE_HID_DISABLE_HUMAN_INTERFACE_DEVICES=1

Beyond that the issue might be fixed by adjusting the scaling of your Linux desktop, opentabletdriver configuration, or Bottles configuration related to scaling or mouse acceleration