I've read that the factory machines the crankcases of the 999 Testa engine at the rear to squeeze it into the Monster S4Rs chassis, which I understand to be based on the ST chassis, though obviously with a few changes.
From an early S4Rs review in Motorcyclist, online
here:
And though the S4Rs engine is essentially identical to what you'd find in a standard '06-spec 999 and 999S, there are subtle differences.
With no room for the 999's 54mm throttle bodies and shower-type injectors, this Testastretta twin inhales through new 50mm bodies fitted with hybrid, 996-style injectors. According to Project Engineer Giulio Malagoli, the only other differences are massaged engine-management software, new cylinder-head covers and some aluminum milled off the crankcases to make room for the Monster's single-sided monobraccia swingarm.