Windows Smartscreen uses a reputation-based system that is extremely disadvantageous to small developers, and there isn't really a ton Toby can do about the software itself until enough people manually bypass the Smartscreen blocking menu (which tells some MS cert reputation server), to pass some unknown threshold.

Here's a pretty good overview of the problem.

As for the uninstallation bug, Fox says he made the executable using game maker's executable making wizard, so the problem I would argue is with Game Maker itself unfortunately.