Maybe you could build the bathrooms and kitchens along partition walls that have space behind them, so pipes could run above the floor, between walls, to the building core where all the main plumbing was designed to be.
It isn’t, it’s called core drilling and it’s extensively used in commercial buildings with concrete decks for electrical conduits, electrical poke-thru devices, plumbing pipes, hot water/chilled water piping for HVAC, data cable sleeves, fire sprinkler piping, etc.
A typical commercial building floor is concrete in a metal pan that has tensioned cables in the concrete to reinforce it. A few holes aren’t going to ruin the structural integrity. A ground penetrating radar scan should be performed prior to drilling to avoid cutting the cables, if you cut one of those, then the structural integrity is affected and repairs get expensive.