The title basically covers everything. I can install the extension and it works wonderfully, but when macOS (Sierra, but also latest High Sierra) is restarted, the extension is gone.
After installing it again, everything works fine and installed styles are retained, but at the next reboot, everything is gone again.

One thing I tried is removing al Safari extension files, as per https://discussions.agilebits.com/discussion/48756/safari-extension-gone-and-deleted
but to no avail.

Also note this only happens with Stylish in my case, other installed extensions don't share the same problem.