Underground stations cost a fortune. I would think a short tunnel for the fast services under Bedford would be a far smarter idea, leaving everything on the surface to call and ensuring platform faces on the MML slows (today's fasts) - that might give enough capacity to share with EWR.
Currently though, you'd see:
4tph via dive under (2 Notts, 2 Sheff)
2tph call at Bedford on surface (2 Corby) + EWR through to Cambridge + talk of a Leeds starter / OA service from EWR?
but there might be a future where more demand is needed to call at Bedford, which might render the works for a fast passing tunnel less viable. Unless it was maybe single track, but then the junctions and signalling for that carry additional risk, even if the TPH could work.