Without seeing what you actually have, you will not be able to determine what needs to be done.
You either have a spigot elbow (no riser), and if so, it won't work at trying to lower things, or, you have a conventional elbow with a socket on it and a riser glued in. If there is no space on the riser between the two sockets (i.e., they're tight together), you can't really lower the flange. You MIGHT get by by cutting a bit off of the toilet flange's socket and the lower one and using a shorter riser, but that's not a given.
You also really need to know if the slope of the existing pipe will allow you to depress it a bit. Otherwise, you'll be forever having to plunge the new toilet to overcome the fact that waste doesn't flow downhill on it's own.
NObody ever said remodeling was always going to be easy. It may take a bunch of tear out and redo to make it all work. Sometimes, you get lucky. Sometimes, you don't.
Last one I did was in cast iron and the 4" pipe was tight up against a plaster ceiling...a major pain to relocate without damaging the plaster beneath. Drywall would have been a piece of cake.