You are absolutely correct about exercising in the money calls is not optimal under ordinary circumstances.
The problem we face, though, is the retail margin requirements.
For example, if we do a 10 lot 95-100 bull put spread, and we deposit $5,000 to cover the margin requirements. Let's say that we get put the stock. Although we have the 95 puts to protect us, Reg T makes us put 50% margin for the initial buy. So this blows margin up from $5,000 to $50,000 to cover the purchase of the stock. Now retail margin rules does not give us favorable margin treatment even though we have the 95 puts and our maximum risk is only $5,000.
Three things can happen:
(1) IB margining system kicks in and sells out the position.
(2) You have enough margin but cannot do anything for the whole day because you are waiting for the position to clear during the next day (you have exercised your put option)
(3) You try to leg out the position (of course, you will take on risk here because you have a deep in the money put option and the spreads are very wide).
If you had the ability to exercise options through the TWS, you could exercise the 95 puts and clean up the position. The TWS will just adjust your cash position and remove all other positions.
I know that options exercise occurs at the end of the day. I am not disputing that. However, this shouldn't be a problem because once when you exercise an option, it becomes irrevocable.