While it might have been 6 miles shorter and a little flatter, it wasn't necessarily going to be easier to the railroad bi-directionally across the lower road. It also got them out of a few heavier population centers, (Augusta/Hallowell/Gardner) with great reduction in frequency through Freeport/Brunswick and Winslow.
I think there are several reasons they opted for the Back Rd.
Operationally, you had:
Back Rd: Oakland, Readfield, Winthrop (there was actually a ~64 car siding under 202 to Annebessacook Rd. Ties still in place), Leeds, Fairgrounds, Rumford Jct. New Gloucester, Walnut.
Low Rd: Augusta, Richmond, Cathance, Brunswick, Sodom
That's 8/5 for sidings over 50 cars (meet worthy), 9/5 is you count Danville.
The Back Rd option allowed them to rationalize the Kennebec River Br in Augusta, the Low Rd option would have required maintaining that bridge, as well as the one over the Androscoggin in Lewiston/Auburn.
It successfully withdrew them from downtown Augusta, Hallowell and Gardner and dramatically reduced train traffic in Freeport, Brunswick, Winslow. The last 3 especially but all 6 in general are, with apologies to anyone who lives there and would take offense, "yuppie." When you look at modern crossing protection these are the areas where quiet zones are put in place. Its an expense and a hassle to deal with this, even if the town pays for upgrades, the railroad has to maintain and pay a higher electric bill. Thats after you get through all the legal shennanigans of dealing with the town. No similar reductions would have been accomplished in ceasing service from Leeds to Oakland.
As for customers on the Lower Rd, they maintained contact with the Lewiston Branch and Rockland Branch. By '87 the Cobbosseecontee Branch was a thing of the past. It's not even listed as an RT by that point. The actual Lower Rd. Main had nadda for customers in the area no longer serviced. The Rockland (and Lewiston) Branch turned into a real winner, there's some big business there now...In the long run, I think the decision to retain the Freight Main was a good decision on an economic level, and 6 extra miles and a few grades doesn't make that big a difference, especially back when fuel prices were <$1.00/gallon. It might make a bigger difference now, but not in the late 80's.