As I've mentioned before, I can basically understand the fundamental reasoning behind tossing everything into FR (BRAND, BRAND, BRAND, BABY!), and I don't think it's automatically flawed or wrong. Tiamat appears in FR because Tiamat in FR will sell more books than Tiamat on Krynn. They do it in a way that doesn't wreck FR, it works fine.
It is a bit of a missed opportunity w/regards to their other settings, but I also think it's unreasonable to expect WotC to choose to sell less books to use the most thematically appropriate setting when they can stick it in FR and it'll be fine. Maybe not as good as it could've been, but fine. A sensible business decision.
I think the reason we aren't seeing more FR-branded threats is, again, the same reason Tharizdun is showing up in Faerun: FR is the Generic D&D World where All D&D Happens at the moment.
I'm not personally one for generic, and I'd like them to focus more on what each setting is actually good at (FR isn't "generic", everything is specific), but if this approach gives 5e greater longevity and means that more niche weirdness (liken Al Quadim setting!) might be published, it's hard to knock it too hard. It does little actual harm, which is a far cry from 4e's sacred cow bar-b-que.