Why do plumbers do this?
Because they don’t give a sh*it.
LOL!
On new construction the placement of the toilet is already etched in stone by the time the plumber arrives. IMO the fault is usually equally split between the owner and the prime contractor. Typically the owner doesn’t want to spend the money for a professionally drawn set of plans. Sometimes contractors talk the owners into going the cheap route, where the part time custodian at the local lumber yard draws up a rough foundation plan and basic floor plan. With today’s modern CAD systems the floor joist can easily be adjusted during the design to accommodate the plumbing, HVAC, etc. Don’t forget the homeowner who requests the contractor to move a wall after construction has started. Don’t think for a minute I am taking sides with the plumber, they make plenty of mistakes, but they have to abide by the laws of gravity when installing drain lines.
Beware of Plumbers with SawZalls… Be very afraid… 
Why did the framer use the wrong hangers?
To keep home inspectors in business…
Worth repeating.