It's really the fault of the county.
They tried to eminent domain from the railroad. Even though the RR had no objection to it, the municipalities did, and challenged it.
The county could have waited until the RRs turned ownership to the municipalities (as was planned) and then maybe the county could then have eminent domain-ed it from the municipalities.
You have to understand, the southern part of Lancaster County is another world unto itself. It is largely ignored, and they seem to like it like that. So of course there was objection when the big hand of guvmint swung in to take land that they thought was theirs. Unfortunately this was a waste of the county's time and resources for a predictable outcome.
Then you get into the bridges. While they will probably stand for another thousand years...some are pretty tight, and won't allow passage of trucks or the combination of two vehicles. So they were declared historic, in an attempt to prevent the trail from being broken up.
It is a mess.