Ty, sparr, that helped.
The mod indeed changes the belts in an instant blueprint in editor mode. However, fixing this is a bit difficult. Although we can detect that Editor Mode is active, it's hard to correctly detect the difference between belts placed by the player and belts placed by an instant blueprint.
I could disable the mod altogether in Editor Mode, but that sounds a bit overkill, and doesn't fix the issue, but rather circumvents it.
For now, I'll leave it as it is. It is still possible to toggle the mod on and off, since this option still works. Just use the GUI on the top left corner (it may be hidden behind the editor GUI) to toggle the mod on and off, or use the default CTRL-B shortcut.
I will update the mod homepage with this info.