Well, Sommurluv, full time pens change the atmosphere . We've done that. It is a lot harder to catch them in their "home" than it is in a temporary exercise pen. For one thing, all the running and jumping around they do when we let them out, they don't do if they are out all the time. It's kind of like kids in a play ground. You let them out and they run and play like crazy but if they were in the play ground all the time, it wouldn't be special. Plus the rabbits "claim" the territory and if you try to catch them they view you as an intruder. With a temporary run, although they like it and love to run around in it, it isn't "home" so when some big person comes after them, it's not like the panic they feel when their safe place is being invaded. This is my observations for raising rabbits both ways.
When we had ours loose in the pen, we used a fish net while we were feeding them for them to get used to it. That was the only way we could catch a lot of them and even that wasn't easy because they will need places to hide in order to survive which means they will be able to hide from you as well.