Yes, that is done frequently. However, if you have access to the floor joists (a basement or high ground clearance), you can apply the PEX directly to the bottom of the existing floor. Holes are drilled in each end of each joist, as near the floor as possible, the PEX is snaked through the holes and a reflective piece of metal is nailed or screwed to the floor thus holding the PEX against the floor and keeping it warm.
There are manifolds for making zone heat for each room and there are modern boilers that are much smaller than the old beasts and much more efficient. Some have even used a high efficiency water heater.