One of the reasons for the short stroke is to keep the engines compact.
Being multi cylinder engines they have large piston areas.
The porting is optimized for torque over a large rev range.
The old V4 90 had a flat torque curve from 4000-6000rpm. The revs boats cruise at.
The newer ones are pretty much the same.
Thats where they have the advantage over the four strokes that only have a flat curve from 5000-6000rpm.
And the two stroke peak readings are higher as well.

BRP got cleaver when they released the engines. Most parts from 40hp- 200hp are the same.
Pistons,Con Rods,Injectors,Heads etc.
The 40hp twin is half the 115 V4.Same heads
The 90hp triple is half the 150V6.Same heads.