I'm not saying it impacts my use of the product (I did say as much in the original post). I am reporting this for two reasons:
a) According to previous information from SmiteWorks, the Steam library is not intended to work this way; instead, the DLC should have both game versions as their parent. It's looks like a bug, so I reported it.
b) If SmiteWorks discontinues FGC some day, and removes it from Steam, then Steam will not recognize that a FGU user has bought DLC that was associated only with FGC. That affects bundle completion at least and might cause some users to buy already owned DLC for a second time at worst.