Difference to X cursor sounds weird.
Hatari uses relative mouse events reported by SDL (SDL provides also absolute mouse co-ordinates, and while those would help with some cases, they could be worse for others, and would be harder to handle in Hatari).
Only thing that I think could explain the discrepancy with X cursor behavior when using real mouse vs. trackpad would be SDL accessing input devices directly (e.g. with libinput) instead of going through X.
According to Ubuntu package database, 18.04 uses latest SDL 2.0.8: https://packages.ubuntu.com/bionic/libsdl2-2.0-0
In v2.06, SDL seems to have added options for controlling the scaling of the mouse events: http://lists.libsdl.org/pipermail/commi ... 01189.html
But I don't know how application is supposed to find out what's good scaling factor. Or maybe SDL apps are supposed just to pass that additional configuration burden to user???
Can you find out which input driver your X server is using and whether that differs from what your SDL version is using?