I haven't looked deeply into update functions, official or otherwise, recently so I am not sure what happens or needs to happen when a dep file is updated.
Some of my thoughts on updating:
I think the dep files in the tce directory that have a new md5 in the repo should be redownloaded as that would assure they are current. Then the contents of the dep files could be updated or downloaded if they do not exist in /tce but exist in the repo. More time consuming, but would provide more stability with dep changes.
But I haven't spent much time updating so that may or may not be feasible time wise.
That would assure that anything added to dep files would be available after an update. Extension name changes are the biggest enemy of a stable /tce directory even when not updating but just using the repo with an existing /tce installation. But that has pretty much smoothed out and with the future change to tcz from tcz,tczl,tczm extension names should be pretty much frozen.