My Subject almost says it all. I have most my engines set to have either 6200RPM max or 7200RPM max, but I don’t want them to shift that high. I’m aiming for the shift points to be around 3200RPM for most of them, but with the ability to get the higher power when needed.
So my question is: Will we be able to set the transmissions for lower RPM shifting? Or should I just limit my RPM to the desired shift point?
Well, in manual transmissions the shift points are determined by the living thing in the driver’s seat. As far as automatic transmissions are concerned, I generally find that the shift points are often determined by how hard you step on the gas. For instance, when I used to drive an automatic, if I gently pressed on the accelerator I could keep the engine under 2,000
RPM for the whole drive, great for fuel efficiency. However, if I floored the gas, the engine would go pretty much all of the way to the redline (and bounce off the rev limiter in a big cloud of tire smoke) 
I’m guessing that the dev team would try and replicate this in game.
An auto transmission would shift entirely differently depending on what you’re doing, if you drive gently it’ll shift up at low rpm, if you floor it it’ll shift up just after peak power etc.
This will be assumed in the economy and acceleration calculations, though of course more sophisticated automatic gearboxes will be smarter about it than old and dumb ones.