When I play 9/6 JoB the expected return with perfect play is 99.54%, I dont have perfect play, I make mistakes, I go for the royal when I shouldn't, I accidentally press deal/draw before I have held my cards, etc etc. How does the casino calculate my theo for video poker? do they just assume everyone has perfect play or do they have some extra for the people who dont play perfectly (like me) If I put $10,000 coin in, would I really only have $46 of theo? (ive never asked for my theo, though I think I will next trip)
Each casino does things a little different, in general though the theoretical will be based on the game & house edge. They do not take into consideration the players "skill level" at any particular game. The game you reference above offers one of the lowest house edges of any game in the casino, so low in fact most casino's will not award comp's at the same level as other video poker, and in fact, there are some that don't even grant comp points irregardless of the level you are playing at. But yes, I would say, $50 or so would be about the correct calculation.
It's no different than the BJ player that stands on stiff hands against a 10 or doesn't double down properly etc. He's just giving the house an extra advantage. I would advise learning the game you're playing better to avoid giving away more money than necessary.
Very few people play with perfect strategy, but if you are doing this on a somewhat regular basis, that's not good. I did it a couple times (as I'm sure most players have) so I made a rule that I would never look at the TV or respond to anyone unless I was between hands or had already held my cards. I would really make a point to try to cut down on this, as it could cost you some serious $$$.
Each VP has it's own theo calculation based on the games it offers. It's very possible that even though you are playing a 99.54% game, that the machine is set to a 1% HA.
In all likelyhood each machine has its own theo assigned to it. And the theo assigned could be higher or lower than what your actual game is paying.