How exactly would you suggest Apple interleave windows from iPadOS and macOS?
You have one mail app, one Safari app, one Music, etc. So the common programs are no problem. If you are looking at the Cornell bird call program, if I open that it should open in a window sized as the iPad app does, or maybe start at phone sized. (I do not have an iPhone, so I don't know what it looks like there. The phones don't all have the same resolution (do they?) so the app must have some capability to size appropriately. So the app is just another window, possibly with a fixed maximum size. Sort of like the widgets they brought back.
Since iPads do not have phone capability the security concern to protect the phone function from malicious interference isn't really there. The screens are big enough that the cramming you need to do on the phones doesn't matter. It should be just MacOS with touchscreen input mode and keyboard input mode. The pen should work in both.
Looking at my iPad (not a Pro, and no cellular) I don't have that many iPad only apps. The birdcall program, (Merlin Bird ID), PlantNet (Take picture of plant, get ID once back to wi-fi range), Freeform, that's about it.