OK; Messrs. Moldover and Newpy, I get it where you're coming from with the lack of passenger train interference (well, freight interference in the eyes of the two sponsoring agencies).
Using this
map as a guide, now I see that Topper would operate on the B&A only as far East as Worcester, then head North on the "route of the State of Maine" to his existing facilities at Ayer. The "T" only operates West as far Worcester. The "T" would actually benefit on the "to be" Berkshire in that there would be less traffic Fitchburg-Ayer.
Now insofar as Lowell Jct to Haverhill with the "T" and on to Portland with NNEPRA, it would appear that is the only area in which there could be conflict. Somehow, I don't think the NNEPRA has the "clout at the State House" that does the "T". Besides, you noted that Chessie will be paying to have PTC installed, from which NNEPRA ("Downeaster") will benefit.