You can plane them down to a flat surface that matches and then install sub-floor and tile.

If you take off more than about 1/4 inch you should sister the top of the joist to restore the strength.

If you have cracks, you have movement.

thats the FIRST issue you need to rectify.

where is the movement coming from ?

was the tile installed over a mud bed or backer board ?

if not, is the thickness of the playwoood and joist thickness and spacing enough to adhere to the L/360 minimum industry standard deflection rate ?

you certainly could mud the tiles in, starting at the high point if there is variance in the height (waviness), but that is difficult to explain in text on a website.

another consideration of a topical solution are the transitions. They finish height of the new tile compared to the finish height of the other flooring surfaces it meets, usually at doorways. If you need a flush transition, you need to do a bit of planning. If its not much of a concern, you may be able to use a doorway saddle. Most use marble for this or hardwood.

Thanks.

The cracked grout was directly above the 3/4" T&G seam over a high joist. No mud bed or backer board.

Floor rated at L / 522.

I don't mind using a doorway saddle because eventually I would like to have either hardwood or tile throughout the home. I just have doubts that goal is a obtainable with my uneven joists.