I'm assuming you used a script to place a clone in the game and to give it equipment and a behavior package. If you start a new game and choose a completley different looking character would the clone come out looking right? I'm just thinking out loud, but could this be adapted to have a PC Clone appear in the game after completing a quest or something? I was actually looking at a way of creating an "Evil Twin" to the PC a while back but never knew about this method.
The way I did it was using a quest and/or scripted object to call a 'Set TwinREF to Player.PlaceAtMe 7 1', then some TwinREF.AddItems to give them a predefined outfit and gear, and finally a set of TwinREF.ModAV commands to bump up their skills and stats. Any scripts go right on the player base object in the geck, isolating the OnActivate with IsActionRef Player == 1. AI packages also go right on the base player object, with a condition of GetIsReference PlayerRef != 1. I used a quest to hold variables that are updated from the clones scripted ShowMessage menu, and the AI packages use a GetQuestVariable condition to read that and change behaviors. Set the quest item and no low level processing checkboxes on the player base object so your clone doesn't get removed at cell cleanup, and so it doesn't forget what it should be doing if you're not around. You can set the AI Data right on the geck page too as changing those won't affect the player. Any inventory you add on the npc inventory tab will always be there at the start of a new game.
Yeah, as long as the clone is created dynamically with PlaceAtMe, it will always have the players current FaceGen settings at the time it was created. You could very easily have a player clone show up after a quest, or upon getting a perk, or pretty much anytime. A clone is just a regular old NPC that was created a little differently, that's all. It still does all the same stuff NPCs do. The only precaution is keeping any base object changes from interfering with the player, which honestly hasn't been anything close to as difficult as I imagined it would be.