It's only more confusion if you're the Governor of New Hampshire. Milepost-based exits work the same way everywhere else in the country and damn near all over the world, so localized confusion quickly gets smoothed out by rote consistency. Believe me...Massholes didn't invent bitching about changing over from sequential to MP numbering. This is a time-honored tradition in every state that's made the flip. Confusion never ends up lingering.I would argue that having them continue logically past the split on both roadways could accidentally result in more confusion. The exit from I-95 to Route 114 would have the same number as the exit from 128 to Route 114 but go to a different place (they're equidistant from the split). Having the exit numbers restart at a different place makes that problem far less likely. That said I'd put Mile Marker 1 at the split since the rest of 128 is toast.
This will be interesting, however, if we actually correct some of our bugfuck Interstate wayfinding. If I-93 ever gets re-routed over MA 3 that's going to resequence everything. If US 3 gets re-badged as I-293 between Burlington and Manchester that'll resequence everything in-state. If MA 24 gets I-x95'd from Westport-north but NOT the disconnected Fall River-south rump that'll resequence everything. If they ever clean up the flagrantly illegal 395/290 mess in Auburn (290 Waterford, CT to Leominster swallowing 190? 490 E-W between Worcester and 495?) that'll resequence everything. But...we're also not the first state to go through that dilemma and come out of it sans Civil War.