you can deal with excess items in the depot (add an inserter and a chest for every wagon). That's why there is a five second inactivity delay when entering the depot.
LTN, at this point, is pretty much complete. With the updates to use the schedule API, you can now keep your interrupts if you want to. Any other change would require a major rewrite of the internals and I am with @optera here that this is better a new implementation than trying to shoehorn it into LTN as is.