It shouldn't, but it certainly will: many people are still in the habit of looking on the board for the Huddersfield stopper because they're going to Huddersfield- the same people who needed reminding at Huddersfield that all services from platform 8 will get to Leeds quicker than the one that says "Leeds" on the front.
This is simply a failure of information. The answer is to improve the information - it isn't a reason to upgrade the capacity of those services.
If we think about the market that the services might be serving (depending on the exact details of the timetable, yet to be published), it could be something like:
Manchester - Guide Bridge (fastest service) *
Guide Bridge (Glossop / New Mills) - Huddersfield and Leeds (if overtaken, these passengers may change at Huddersfield)
Manchester - Stalybridge *
Stalybridge - Marsden/Mossley
Stalybrdige - Huddersfield and Leeds (if overtaken, these passengers may change at Huddersfield)
Marsden/Mossley - Huddersfield and Leeds (if overtaken, these passengers may change at Huddersfield)
Huddersfield - Dewsbury*
Dewsbury - Leeds *
Mirfield / Batley / Morley - Leeds
Manchester - Dewsbury
Manchester - Mirfield / Batley / Morley
Local flows between Dewsbury and other Huddersfield line stations.
It seems unlikely there will be many people using trains for other local journeys because of their skip-stop nature.
The exact timetable will dictate how much Manchester <> Huddersfield, Huddersfield <> Leeds and Manchester <> Leeds passengers use these trains. Hopefully it will be very little or not at all.
*Large number of alternative services
And at peak times there will also be the Northern services serving Stalybridge - Huddersfield inclusive.
Bearing this in mind, will it really be full as a 3 car service?