318 4 bbl and intake upgrade

Port mismatch matters. Port mismatch doesn't matter. Both are blanket statements that have exceptions. Not saying in this case it will matter but in some cases it does.
Chrysler did a lot of things based on the constraints at that time. Such as cost, availability, time, emissions, politics and performance to name a few. That caused a lot of compromises to be made. I don't think that just because Chrysler did it that way means it couldn't be done differently or even better. The OP has lots of options.
I agree with all of that. I think as the combo gets more racy, the mismatch will matter more. On a stock or mild engine, I don't think it will ever make a difference.