They're using the Dual Modes because those are the only diesel locomotives that have enough HEP capacity for the 10 car multilevel trainsets that will be used for the service.
Running at normal rated track speed they cannot handle 10 MLV's worth of HEP in D-mode. The 45s in D-mode can supply HEP for only upto 8 MLVs. That is the reason they are not going to be deployed on through Bay Head to New York rush hour trains (i.e. there will be no through Bay Head - New York rush hour trains), because it is essential that the rush hour trains be 10 cars on that line. This come straight from Kevin O'Connor Chief of Operations at NJT. Also, at present there is a significant shortage of 45s since fewest of the damaged 45s have been fixed of all classes of engines. My guess is PL42s will be used in preference to 45s.
The 45s can handle HEP for 10 MLVs in E-mode.One possibility is that they might use 45s at very low speed low acceleration run from SEC to Meadowlands, to be able to feed HEP for 10 MLVs, just as a special case. Or in the winter they could simply let HEP trip off specially if it is not too cold a day and run the trains without HEP. That would be an interesting data point
I would have had a lot more to say if you hadn't clarified with the second paragraph.
However, from a specification standpoint, the HEP rating for the 45s is 1000 kW regardless of mode, while the HEP rating for the PL42s is 800 kW.
Yes, if you siphon off all 1000 kW to HEP whilst the 45s are running in diesel mode, you only have enough continuous tractive effort to achieve a balancing speed that is relatively low, which is why they would not normally run 45s in diesel mode with a 10 car mlv consist for a longer scheduled run (as it would undoubtedly cause delays in the schedule). But for a short jaunt between SEC and the Stadium, it is acceptable. Not to mention, they've been running 10 car MLV shuttles powered by 45s whenever the shuttle service has been scheduled to run for at least the majority of December.
You also fail to acknowledge the fact that this service is going to be run on a weekend. Most of the 45s that are in revenue see service on the weekdays and are mostly restricted to the Hoboken division. I foresee no major complications that would prevent them from pulling 5 or 6 dual modes that would otherwise be sitting idly at the MMC on a Sunday, plus 50-60 MLVs which would also be sitting idly at the MMC on a Sunday and putting them to work. 5-6 consists max should be plenty to keep a roughly 10-20 minute departure interval for a run that is scheduled on paper to take somewhat less than 15 minutes one way. That would place 1-2 trains idling at each of the respective terminals with 1-2 trains on the road between the terminals.