Back to the original question:
I consider the 2-seamer and the 4-seamer to be different pitches.
If your son can get to 90-91 with his 4-seamer, that's a valuable weapon to have in his arsenal. He should use it.
I wouldn't throw it down the middle or anything, but used in proper sequences and locations it is a pitch he will be able to use with great success.
He should definitely use both pitches regularly. This will help him both now and for whatever future he may have.