Putting aside the Duncan comparison (which I get why you made, but I just have Duncan top 5 all time so I don't wanna squabble about it. Duncan > Shaq, Hakeem, Wilt, Bill Russell, imo), I do think there are similarities in that.
Now, Duncan did transition to playing the 5 more towards the end of his career, and maybe AD will do the same, but I seriously do think it's a mental thing.
AD seems to think that positions require certain playstyles. He plays a more face-up game, does more ball handling, shoots more from distance, and has a relatively small focus on the post game for a traditional centre, and for him that's the game he thinks he would be expected to play if he was listed as a 5. As a 4, his style of play is more typical historically (especially if you remember that people like Bird actually played a lot of PF in his career), and he seems to feel better when his playstyle fits that expectation. I think he's afraid that if he is listed as the 5, he would expected to be someone that he isn't.
Obviously that's not true, and in today's NBA centres are not expected to be play like Robert Parish, but if it's a mental block (which I think it is) then what can you do about it? Not much. Just play him next to a PF and list them as the centre instead, and let him pretend he's a PF while he does the C job all day.