Alternator - regulator mismatch?

Actually resistance in the charge line does not cause regulator / voltage problems. In fact as long as no accessories are sourced from the charge line, the only thing that causes--within reason--is heating up the wire. Of course it can become a problem in just that way.
It shure does. We agree there is resistance.
We agree the regulator is only going to know the voltage at its 'i' connection.

Any resistance between the power source and the regulator is going to cause a voltage drop.
It doesn't matter if the drop is in the alternator output line, in the ignition switch, or the bulkhead connections.
Since the voltage reduction varies with current, resistances in the output line can cause the regulator to see much lower voltage than the alt is producing.

Now as far as the battery goes. That I agree will not see excessive voltage from resistance in the output wire. If that's what you're thinking about - battery charging - agree there.