EMRY is to Irving what MM&A Canada was to Rail World. Its a property owning, non operating subsidiary founded in the other country for taxes and property rights.
MNR was created because who knows why but I'd wager it had to do with requirements laid out in the bidding process. As far as I know MNR owns no land, I think the stretch from Madawaska to Van Buren was sold to EMRY. CN still maintains the WC corporate entity and a few other American subsidiaries for operations in the US. In terms of organization in railroading, most border crossings involve 2 railroads at the paper level, even if only 1 at the practical level.
There are all sorts of reasons companies maintain reporting marks, and corporate entities. Taxes, labor agreements yadayada, if you want an iron clad reason, I'd suggest you write to Mr. Fink, at Pan Am, or his counterparts at VRS, or JDI and ask them, because outside of upper management, their legal and economic teams no one is gonna know. But if its done, its done for a reason.
Reporting marks and Marketing are also 2 different beasts. BNSF still owns and uses the ATSF, BN, GN, NP, SLSF, CBQ, and SP&S reporting marks, and uses most of them on their rolling stock fleet. Union Pacific still has countless cars running around in old marks, but you can be sure when a unit train of old SP hoppers shows up at a mine, the shipper dealt with Union Pacific's marketing department. Likewise, "Vermont Rail System" and "New Brunswick Southern" are marketing names. I don't know, but I would speculate Irving, and VRS, have a single marketing department, where their railroads put in a single marketing package.