can strongholds quests do in later chapters not in 2nd or 3rd

Yes, but you really want to do them as early as posible because most of them have a significant mini-plot to run through and so youll either miss it or spend weeks waiting for things to happen if you do the strognholds later.

You can also do them in sixth. If you get Nalia's castle, though, even if you're in the UD or SH, you still get gold every week.