I assume the notch right before S. Acton going outbound, where it intially turns single track, will be a bottleneck - I'm not sure there's room for two there, but I've only seen it from inside the train.
Part of the pain of the single track is that S. Acton is also a terminus for several of the trains - thus blocking all traffic while waiting for turnaround, lmiting the schedule. There is no outbound train between 1:20pm (or therabouts) and 4:40pm that goes past S. Acton.
They'd probably have to rebuild the platform at Littleton again to push it back, or finally move it like they've been talking about.
I did take a late outbound train that had to halt at Waltham due to a signal - for quite a while. Apparently the controller forgot about us...
First Law of Public Transportation: You can never be early, but you can always be late.