Gawd it's hard to convey some things over the internet...my failing, no-one elses. I may be totally incorrect and/or may absolutely butcher my explanation of what I'm trying to convey...so feel free to skip right over this one.
Using your picture as a reference.
Assuming that the bevel gear is fixed vertically (by shimming between the mechbox shell) and horizontally (by it's axel), and the pinion gear can move left and right laterally (not exactly for the picture but close enough).
If the pinion gear was jammed in to the left of the picture then the teeth would interface, tooth contact would be solid and the gears would probably jam and not rotate well. The amount of the tooth surface of either the pinion gear and the bevel gear would not be the entire surface of each tooth...the tip of the pinion gear teeth would be past the inside edge of the bevel gear. Back it off a bit and you've probably hit a good sweet spot.
If the pinion gear was backed off way to the right...tooth to tooth contact would be minimized to the point where it was just the edges touching before they miss each other all together. In the reverse of a jam fit, the widest diameter part of the pinion gear teeth would not make contact and very little of the rest of the tooth would...and I suspect that's why we see so many motors with mangled pinion teeth, but the lower part of the teeth look pristine (sometimes the black oxide coatings aren't even touched).
Now imagine your reference picture with the pinion gear still fixed in the same horizontal left right axis. But now the bevel gear is raised up on it's vertical axis. As you described, the two angles are the same between the teeth, but now with the bevel moved up, there's no way the pinion gear can advance far enough to the left to fully engage the teeth of the bevel gear. It's essentially forced to be "backed off". But unlike the previous paragraph, the tooth to tooth contact surface isn't just at it's edges...but rather the teeth are jammed together.
If you want to play around with it a bit...with your noisy gear set (no need for anything else in the mech) shim the sector gear and spur gear well and leave the bevel gear kind of loose (not so much that its teeth come off the spur gear teeth or that it rubs on anything) but lose so it can move laterally a bit. Attach the grip/motor, play with the motor height and check it out. You'll notice the bevel gear move side to side relative to the mechbox shell/bushings. Warning - if you power it up and pull the trigger...you may strip your gears doing this...(but I did it anyways!
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Anyways...too bad you weren't local. We could pool the parts are try a bunch of stuff out.
Tys