The intonation on my MB is not perfect. Over 3+ octaves it is noticeable. Usually if I set the tuning to 'Beat' in a pleasing way at the top end of the notes I aim to play, the lower notes sound close enough... but it depends on the patch, and the desired sound.
You CAN alter the intonation by routing Kbd / Seq to the offending oscillator's pitch and tweaking it. If it's OSC 3 you are adjusting, you might also need to route a voltage offset to the pitch (using one of the Macro Knobs) since OSC 3 does not have a Fine Tune control.
You might have to go back and forth between adjusting the Kbd /Seq to Pitch (with a high note held) and the Pitch Offset (with a lower note held) to get it just right.
On mine just now, for example, in order to get Osc 3 to track better against Osc 2, I set Macro 1 to +50. With Kbd / Seq > Osc 3 Pitch at +8 and Macro 1 > Osc 3 Pitch at -8, they are pretty damn close all the way up the keyboard.
EDIT: I should add that, in duo-split mode, it's a little more complicated than that. The Kbd / Seq in the mod matrix follows whichever side of the split has OSC 1 assigned to it... so trying to match OSC 3 to OSC 2 with my method won't work if OSC 1 is on the other side of the keyboard split. You'd want to pair OSC 1 and 3 together, and have OSC 2 on the other side.