That agent was either incompetent or high. My bet is on the former.

AR42AP does allow, as per your post, a free stopover and it prices just fine on ITA Matrix. And I don't see any major price difference.

I would ask them to make a dummy booking with the same fare and see what it comes out to. And ask to speak to a supervisor if they still maintain the position that it would incur a hefty repricing.

Again, people put way too much trust in these folks. I think the folks at the daily mirror are a better source of the truth than customer service people.