Thanks mate, because I am using shellac, I find it easier and more manageable to stain/French polish the body and neck separately, and then cleanup binding etc before glueing the neck.
Also, I will be spraying on poly and then applying wipe on poly. So for me it would be easier to spray the neck and body while they were separate and then glue it. After they are glued, I would still need to do some touch up on the finish. Knowing me when clamping the neck down to be glued I would mess the finish for sure in some areas.
So I guess in terms of “best practice” it comes down to what kind of finish you are going for and how you go
About applying it, I think it can be managed either way.