The pokemon IVs are still generated the old way, and with the power items, those IVs are passed no matter what with the rest generated the old way. So that can cause problems, but there is no change in the breeding.This allows you to send up to two Individual Values to your baby Pokémon, leaving the rest determined the same way as in the past with some random and some selected randomly from the parents. However, if you do it with both parents, you will not be able to control the baby's Nature through the everstone method.
Syberia tested having 2 parents with a different item each and see if both IVs would pass along with the average 3 from the 2 parents, but resulted with just 3 IVs passing each time. This proves that holding the power items only force those IVs to pass and 1 is still passed from the parent, and the last 3 generated by the breeding RNG.