I don't know how things are in other parts of the country but here in IL, a furnace inside the home and an a/c outside in the backyard are a split system.  And one can be installed completely separately from the other.  If they each otherwise qualify, you have up to $1200 in credits.

Think of it this way.  You could do the ac in 2023 and because the cost is obnoxious, hold off on doing the furnace until it dies in 2025.  No question there about two credits. 

As for the paperwork, see if they can write it up as two projects.  Or if not, allocate the labor on some reasonable basis.  Or maybe the cost of the units themselves are such that the labor component is irrelevant.