My son was in a similar position when getting recruited. He was looking at some of the high academic D3s but not quite Ivy level. He has always been a MIF and a closer (although in HS, he played SS but did not pitch much despite hitting 88mph on the gun in his senior year), During the recruiting process, he always focused on explaining his tools and saying he was willing to play anywhere the team needed him but told the absolute truth about his desire to play MIF and pitch whenever the team needed him. What he consistently heard in return was, "we recruit athleticism. We like kids who play up the middle and can adjust to where ever we need them." All of the D3s told him they would consider him a 2 way guy. The D1s only saw him as a MIF or at 3B. The D2 that he ended up at saw him as a 2 way guy.
Now, he is a Freshman just starting fall ball and the HC has him working out with the pitchers and the infielders (BTW: the current HC is not the one who recruited him). There is only 1 other guy on the roster who works both ways also. It makes a tough schedule even tougher but he reports that he's enjoying the work and looking forward to seeing how he can help the team best. The way I see it, it gives him more options to contribute and to be ready for whatever comes next.
The best advice I have is to stay flexible, focus on advancing all of his tools, be completely honest with yourself about his abilities and ask as many questions as he needs to in order to make the best decision possible.
Good luck to your son on his journey.