saving the game with mods once sets a flag such that if you open it in vanilla later, it will warn you that mods were previously used. maybe that is what those people were worried about?
if you use mods to create vanilla buildings that are in an invalid state somehow, that could theoretically persist even when the mod is uninstalled, because it's saved in the vanilla building. have only seen this happen with Smart and Mass Upgrade when it creates broken belts. even in that case, you could use a tool like SCIM to remove the corrupted belt