I've recently discovered the magic and convenience of quest aliases and was wondering...are there any drawbacks to Forcing refs into aliases via scripted spells?
Personally, I don't see many 'drawback' while using Aliases and Forcing Aliases via scripts. The only 'drawback' I had was some flaws in my designs. I have to call 'clear()' on alias before forcing it again. (better be safe than sorry?)

As I understand it persistence concerns only happen with aliases that are filled with a specific reference and not ones that get filled on the fly?
They are both 'persistence' from what I understand.
Aliases 'filled on the fly' as you put it, they are picked in the loaded area (persistent) or specific Form (permanent persistent)
Object/Ref that are unloaded (its 3d, model removed from the cell or memory) become non-persistent.
Actors can be in any number of aliases? or will having an actor in multiple aliases mess things up?
Actor can be in several aliases. Usually, the one with higher quest priority 'wins' over. Not sure how aliases with different mods behave, but my wild guess is that mod loads later will win over.
By win-over, here is my examples:
- I have 2 quests running, both have 2 different Aliases point to the same Follower (Lydia for instance)
- If these 2 Aliases have 2 separated 'AI Package' running, the one with higher quest priority will win
- Other scripting behavior seems to behave independently, regardless of quest priority.