What was the position of a program that resided in the matrix when compared to a machine in the real world? Were the machines of the real world superior? If yes, why? If no, then what was their position like? Did the machines even have notions like that?
Each program in the Matrix was an AI. They were all designed to perform a task and to be intelligent enough to learn and self correct in their daily activities. Each AI in the Matrix was distinct, and, the ones that had feelings for sure like the Merovingian by virtue of being a unique intelligent entity definitely must have felt much different from any of the machines on the outside.
The ones that may or may not have feelings that a human could relate to, like The Architect, don't "feel" different per se, but their modes of operation are unique as these are intelligences with personalities that can reason we're discussing.
Other than the Deus Ex Machina, it's unclear from canonical sources I've seen if the machines outside of the Matrix were even self aware. I don't think that the ones we saw in the film were for the most part, or they would have done something other than blindly charge the Nebuchunezzer and get EMP'd.
It follows that an intelligent machine would have either encountered hostility like this before and planned an attack whereby only half of the aggressors were in range of the EMP and the rest could then finish off the enemy. (They'd know from previous encounters that the EMP needs time before it can be fired again.) It also follows that an intelligent machine with understanding of 3 dimensions and flight wouldn't have let Neo's ship go over them. :P