If you are going Aimpoint and you know thats all you want, the #46 will be just fine. It will give you an uniturrupted, continuous top rail to mount the Aimpoint at any point from the rear site to the front site.
I really dont think the #50 is any better, I think its equally as good, just slightly different. If it were me, I would pick the #50 regaurdless of what optic I would be using. If I were putting an Aimpoint on it, I doubt I would mount it ahead of the top rail anyway, and if I did, I would just get a spacer for the aimpoint mount. On top of this, the #50 is cheaper.
I've built guns with either system, the only time I used the #46 is when I was unable to obtain the #50. ARMS was out of them for about a month or so a couple months back. I got the SIR system when it first came out. I bought the M model because I erroneously thought it mounted to the rifle more solidly. So now my gun has no delta ring. If I were able, I would replace my #45m with a #50 tomorrow. But putting a delta ring back on my rifle is more trouble than its worth the the permanently attached Vortex. So I'll stick with the wider, heavier, #45. Really, the differences between them all are slight, you wont be sorry either way you go.