I wouldn't say "unable" to zoom, etc., just a bit more difficult. When GPS is active and depending on the options you have selected, it can be difficult, particularly on the move. This is due to the fact that the GPS is taking readings every second and up-dating the information, such as the position of the map on the computer screen, accordingly. So, just as you, say, zoom into a spot, the map changes the view overriding your zoom. You can do things like adding your current location as a stop by using F3.
I haven't tried it, but I would think adding pushpins or new stops while on the move with GPS active would be a very tricky thing. Perhaps it is doable if you are stationary and if you have disabled "Provide navigation" and "Arrange map view:" if that is possible.
With regard to your question
If I had a second window on which the same saved map was loaded would I be able to switch to that window, add stops or push pins, and then make the GPS active on that map? Would I need to deactivate the GPS on the other window first?
I don't know. You might need to experiment a bit on that.
The main thing that users should understand is that S&T really functions in two distinct modes that may not overlap: route planning and navigation. The premise seems to be that one plans the route before embarking on the route itself and then navigates against that route over the road. Re-routings are possible while navigating but substantial changes to a route are, at best, difficult.
I can remember driving from Spokane, WA to San Francisco once that I had planned as a two-day route, stopping over-night in Bend, OR. Part of the way along, I thought about doing it straight through in one day. So, I opened up a new window to calculate the route, leaving the original minimized with the GPS active. In the end, I stuck to the original plan but I suppose I could have switched to the new route and turned on the GPS and carried on.