I've read there used to be some issues with using the 'Reinstall mod' option, but it seems to work ok for me)
To get the FOMOD installer to run again you need to select 'Reinstall mod' in the opposite click context menu, or delete and reinstall the mod again from scratch. There's no error message or warning so users may not realise what's happened. It appears to just re-enable the mod, presumably using either the default options or the previously selected options if they're saved. to select different options, the FOMOD installer will not run again.
If you've previously installed such a mod, if you later disable then re-enable it eg. I've encountered this issue in NMM v0.80.0 (and previous versions) when using Skyrim SE mods which contain a FOMOD installer.