You're quite correct here. The centerline of Montauk station is at stationing 6076+30, which is MP 115.08. The stationing numbers that are used for engineering purposes don't change over time, even with right of way realignments! What they do is create "match marks" where two different stationings are "equated." (I think I have that terminology correct!)
The Port Jefferson Branch has three of them between Syosset and MP33, all probably due to the realignment in the area of the sand pit used for Jamaica station around 1911.
Interestingly, even though the mileposts from Valley Stream to Far Rockaway were re-done in the not-too-distant past, that branch's stationing numbers STILL ascend from Far Rockaway to Valley Stream because they originated via the Rockaway Beach Branch across Jamaica Bay and up from Hammel!