This is true. But Reading the op post, it sounds like just parts that went bad because ofyour mods will not be covered (once proven). Although now, it may be a bit of a battle for every repair as they will most likely blame the mods.
As for buying the warranty with mods already on it, it doesn't matter. The terms say any parts that are not OEM equipment won't be covered along with parts that get damaged to the to modified parts.
Hope all works out OP.