No. The MTA is ordering MLV's or MLV facsimiles in a mass replacement for the MNRR Upper Hudson/Upper Harlem flats and the LIRR C3's, with CDOT then getting to mull over how much it wants to participate. That's a capacity thing for MNRR as the most crowded Upper Hudson consists already max out the lengths of their assigned GCT platforms and of the 6-car platforms north of Croton-Harmon, so they can't add more cars to overstuffed consists without creating platform dwell problems. Their solution was to go all-MLV for optimal per-car seating density to lick that problem, and to shoot for best possible unit price point by lumping in the LIRR C3 replacements into one common mega-order stretched well out with trailing options so both roads could get generous fleet increases. Other than LIRR's cabs having the extra cab signal aspects and some being painted yellow for LIRR and blue for MNRR there's expected to be zero difference between MLV's assigned to either road, and they can be shifted (esp. the trailers) from one road to the next if needs change. MNRR is going to need the future capacity expansion options for Penn Station Access-Hudson, and LIRR is going to need the future capacity expansion options for schedule expansion in Scoot territory as well as for longer consists on the remaining post-ESA Penn push-pulls because the next-gen common MTA/NYSDOT dual-mode loco order will allow for hauling more cars per train on a single loco than the DM30AC's are capable of. So for wholly capacity management reasons the MTA board made up their mind that they aren't retaining any flats and are locked into a bi-level future everywhere. Nothing changes for MNRR WoH because the Comet V replacement calendar syncs with NJT's Fleet Plan and won't feasibly happen before FY2025, but it was already anticipated that when NJT was ready to move on a final purge that MNRR would be tagging along on another common order.
The only variable with this new MTA mega-order is how far CDOT wants to go in. They could order MLV's just for the Danbury-GCT & Waterbury-GCT trains to keep the MTA happy, order lots and lots of them to equip the Danbury/Waterbury shuttles and/or Hartford Line, or order none at all because the GCT runs from Danbury/Waterbury really don't tax the 4- and 6-car platforms at GCT running all-flat. CDOT could instead see economy in dumping its oldest Shoreliner I/II cars and the Hartford Line Mafersa fleet (nearing rebuild age in a few years, and can't run into GCT) by picking over all of the MTA's 106 displaced Shoreliner III/IV's with ownership swaps, and going all-in on a unified intrastate fleet of GCT-capable, three-door Shoreliner III's/IV's with more extras piled up in New Haven for future expansion than they know what to do with. They can also use their below-cost ownership swap options to scour all the '09-rebuild Shoreliner I/II and Comet II razorblade fodder for good scrap parts to lower the costs substantially on a light rebuild program for the Shoreliner III's/IV's. So given all that, CDOT does have a lot to think about before it signs on with the MTA's MLV order and for how many because they may get a legitimately better deal playing scrap-n'-swap for a uniform rebuildable Shoreliner III/IV fleet instead of buying new.
I'm not aware of any clearance issues with the Comet V's and GCT. Since the formerly west-of-Hudson Comet II's got moved EoH after the V's were ordered, I would think that MNRR would have vested interest in making sure those things were portable over life-of-vehicle. They can certainly trainline with the P32's because they were already capable of trainlining with the P40's when NJT still had those on the roster. They're fair game with any locos on either NJT's and MNRR's rosters, whether actually paired with certain makes or not. The trailers (not cabs) could conceivably even run with LIRR's DE30AC's/DM30AC's, too, if they had the coupler adapter for LIRR's funky pin layout (which is going away in the new coach + loco orders). LIRR leased a bunch of rote-standard pin MARC II flats to run as summer extras sandwiched between double-draft locos outfitted with adapters to square the differing pin layouts, and it worked fine for them. Just means that the C3's are going straight to scrap upon the MLV replacement order and not seeing a second life elsewhere because in addition to having no low-boarding door traps any midlife overhaul would also have to change out the unorthodox pin arrangement in the couplers.