I completely agree. The details are fuzzy to me but yes, I remember being urged to link accounts as well with the promise of some tangible benefit. I went ahead and did so for FFXI and FFXIV - they are both on the same account.
(EDIT: Ok now I realize why I did this - to get the useless hermes sandals or whatever that ridiculously stupid item was given to have both FFXI and FFXIV active at once)
Then I went to add my buddy pass. And I paused. After I thought it through I realized I would be completely screwing myself over to have two FFXIV accounts on the same ID. Yes it would only be one security token to keep track of and one payment, but it seemed to be a horrific nightmare otherwise (for all the reasons you listed).
So in the end I created a whole separate SE ID for my buddy pass and I am immensely happy I did. They are both Legacy which means I will have two accounts to use in beta![]()
I'm really sorry you're in this mess...........