I've played a few MIM necks in the past that felt thinner than the average MIA neck. I assumed that the MIA necks were slightly thicker to accommodate the reinforcing bars, but I admit that was pure speculation on my part. I admit I haven't seriously played a new MIM Fender in several years so maybe my observations were based on the way things used to be constructed. Perhaps I just happened to get instruments that worked out where the MIM's were thinner necked (although it would be odd that it happened that way consistently). Whatever it is, I also observed a difference in the necks I played much as the OP did.
For what it is worth, I found the MIM necks to be too thin for my tastes and preferred the MIA's slightly more substantial feel.
For what it is worth, I found the MIM necks to be too thin for my tastes and preferred the MIA's slightly more substantial feel.