Correct. Because we have many collections we decided it would be easier to maintain locally on the build machine then to have to maintain the files in each collection. It's too bad there isn't a probing path on the controller like there is on the dev machine.
But you are going to have at least as many build machines as the number of collections so the effort is more or less the same
And to script the update on multiple collections (by this i mean updating the activities assemblies) is quite easy (rather than to log on all machines and update the gac (granted that can also be scripted)).
I understand your scenario and unless i'm missing some data in the medium term (even in the small term) you will be better served by using the custom path assemblies.
You will also have added benefits, like traceability and auditability without any costs or effort.
Just to be clear, not trying to make any judgement on your choices, just trying to understand them.