I don't know, but I only believe there is one pvc pipe and it is on the roof. It has a downfacing "u" at the top and the manual has a figure labeling what looks like it an intake. The City has now chimed in and it says the minimum is 3" if the unit is in the attic, which it is.
AHJ/Authority Having Jurisdiction.
can add additional requirements to any national or international code.
So if the city is saying 3'. Then they probably have a printed version of their code. that you can get a copy of, and show to the HOA. They can not legally force you to violate an International, or local building/safety code.
Although a down facing U is for an intake. Nothing says it isn't the flue pipe, and terminated wrong.
Might want to recheck the piping.
And post a pic of the furnace and its PVC piping.