These are only the basic requirements. The law is more complicated in that exemptions are required by law if another series of items are met.
The only ones that know for sure if CSX needs to implement PTC on the Plymouth Sub are CSX and the FRA.
No surprise if the dwarf signals are being replaced. On the one hand, they're used where speeds are low. On the other hand, being closer to ground level means the chances of them being obstructed are more than it should be.