Howdy. Congrats on the LNIB NYPD 5946 find.
Without being able to actually handle and examine it, I can only offer a couple speculative thoughts on my experience with a lot of other 3rd gen guns.
First, the sideplate being allowed to flex slightly outward might have more to do with the way the grip fits on that side of the frame, meaning allowing some extra room for the plate to stand proud from the frame. Sometimes a grip might not fit snugly against the left side of the frame.
Secondly, as long as the front of the plate isn't sticking so far outward that it allows the slide stop lever's plunger to slip off the plate, to the inside, and no longer support the plunger, it wouldn't worry me overly much.
I've seen my fair share of 3rd gen guns where the front arm of the side plate stood out a little proud from the frame (due to the way the grip wasn't snug). The guns ran just fine in normal operation.
However, can you grasp the top and bottom edge of the front of the side plate with your finger tips and GENTLY try to wiggle it up and down? Does it have excessive movement up & down, or is it stationary against gentle finger tip pressure to move it?
Usually when a side plate is damaged (improper grip installation), it's the little rear prong, of the pair that snaps over the sear pin head, that gets bent (to the rear) or broken off. This allows the front end of the side plate to lift upward, which causes the loss of proper tension between the side plate and the slide stop lever's plunger. The angle of the front of the side plate is what keeps the slide stop lever in the 'down' position until the force of the mag follower and mag spring lifts it upward on an empty mag.
Just to show how subtle a change in the front plate's angle can be, here's a couple pics of the older and newer 4506/1006 side plate angles. They increased the angle just a bit to better help keep the slide stop from rising under recoil.
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Just some thoughts.
No movement up and down. I can press it in towards the frame and it will move in and then back out when I release it.
The grip not being flushed is not the answer, I don't think, because with the grip off the plate still juts out a bit.
I might pick up a couple of sideplates, just to have them. This is now my 3rd 5946, and I also have a 5906. I assume same part number. Couldn't hurt to have them on hand. And I'm eventually gonna take a ride down to the outdoor range and have the guys look at it.