Well.. I did say I wouldn't take about this more, but since you're calling me out specifically...
Yes, you activate XComFiles after playing Piratez and boom, the proper XCF options are loaded. You then decide you want to play Piratez some more, activate it and bam, proper Piratez files. How is that not convenient for like... 99% of users? The only one left would be activate vanilla and vanilla options are reset, maybe, but vanilla options are kind of bad so...
If you load a mod that doesn't have special options (say.. one that adds an extra gun and nothing else) then nothing happens. If you load a big mod with important options, the act of enabling it changes your options only the first time you enable it only. That's pretty unintrusive to me.
Especially since, if you play two big mods, the proper way to change between then is by changing user/data/config folders, not swapping in the mod page (which makes you wait to load mods twice), so the options reset would only happen once: when you start using a new mod, unlike what I described above if you are well organized.
And honestly, if you don't want to use the options a mod creator created their mod for, I think the effort should be yours to break it. It should be as easy as possible to play with the proper options, since that's the right way to play. You want to change things? Fine, but do some work yourself.