It's a PITA to notch the pistons while the block is assembled, but it's been done.
The usual warnings about greasing the edge of the dome, using Mor-Tite etc. to prevent chips from getting loose etc. apply.
You use an old lathe bit re-ground to a 1/16" radius nose and brazed onto an old valve (stem must be same or slightly smaller than the actual intake valve). The cutter nose should be at the actual valve radius + .030" minimum, I prefer .050" to make the actual relief the head diameter +.100". 4 bits make a smoother cut (less chatter), but harder to get the radius to match.
Because of the close distance, the piston has to be away from TDC to be cut (a lathe bit is too thick to fit between the seat and dome near TDC).
When assembled, measure the stem height above the head - use this as a reference for depth of cut.
Lot of grease on the stem, turn the stem very slowly with a drill while applying very light pressure.
The stock dome is thick enough that cutting down .060" won't hurt. Mark the stem at .060" above the guide etc. or you can clamp something on as a stop. If I have to do a few of the same size, I make a brass shaft instead of an actual stem (less wear in the guide) only .001" smaller than the guide ID, and thread the upper end 5/16-24 NF for a fine-thread large diameter nut as a stop, each hex of the nut is .007" of movement.