He won't have "end grain" cuz it's MDF. Splitting the angle in half is the only way to get it correct, especially since your CP only has the two back corners @ 90 degrees. If my guess is correct, those two pieces are for either the side-to-front angle, or the front angle-to-front angle along the front face....there's absolutely no way to get those to match up without the math...do it, you'll thank yourself later.
As an aside, whenever you are using a tool that has "preset" detents, don't trust them....they're oftentimes notoriously sloppy, i.e. the detent @ 45 degrees could actually be off by a degree (44, 46) OR MORE!
Sanding can probably solve THAT edge...hope you didn't do all the cuts at once!