Maybe the heater core went bad soon after delivery and the only core they had available was the 2.5?

If you do not have AC, the 2" is correct, but you pulled a 2.5 out.

Would seem to me that according to the manual a 2" should be there.

The ends are bendable (copper) and can be fashioned either way. As far as them pointing to a particular part of engine bay, there should be no more than 3/4-1" of the ends sticking out of the firewall anyhow. If it does not fit "exactly" the ends can be bent, cut and reflared at the ends to suit your needs.
I am looking at a concourse Ram Air II motor pic and I see the heater core hoses going right to (almost looks like into) the firewall with clamps.
The only parts of the heater core that should be seen prior to installing the hose is the flare and enough length to secure with clamp.

As far as another idea? Call AMC and tell them what you ned and send them your bad core and have them modify it exactly as your old inlet/outlet routing.

All over a $60 heater core that you will not see..

???