I have not been able to set a rally point that is different than just the move rally point. E.g. in the base game if I right click rally point on an enemy building then ungarrison, my spear cav runs over and tries to capture. If I hold ctrl and right click on a building, the rally point does not even register and my cav ungarrisons at the front of the building. I thought I might have to change the autorallypoint from ctrl to a random key "k", but I still had the same issues.
(In my example, I assume that setting a rally point on an enemy building is the same as setting it on an enemy bolt/catapult because I don't know a map that starts with siege.)
In the your mod of game, both of those things happen exactly the same.
I have looked at the default.cfg at https://github.com/0ad/0ad/blob/master/binaries/data/config/default.cfg and also scrolled through the hotkey editor on Autociv and have not found ways to change rally types. I am wondering what you mean by setting different types of rally points.
I see the capture delete meta as analogous to an ancient scenario where troops came into the city and they started to raze the buildings. If the city didnt send troops and waterboys to save the building it would be destroyed. Making the capture any more expensive would make warfare before stage III irrelevant because garrisoning in the cc, sentry towers, barracks, houses is much more cost effective than the attacker sending troops all the way across the map.
The only issue I have with capture delete is that it makes sense to stack houses in front of sentry towers to prevent capture but that doesn't really align with the ancient torching scenario.
Usually people have lots of farms around the cc so I have never seen territory captured that prevented the cc from being rebuilt after it was destroyed (except a case where a rotary mill was captured but that was seen as a bug). If the cc is captured, you shouldn't get another cc nearby.