Point A (or very close to). You need to measure from the top E slot to the point on the saddle slot where the string will sit, which is just a touch back from the front edge.

Yes, the bridge plate sits square and the intonation is all done by saddle position. In theory, the top E saddle will sit about 2mm further from the nominal scale length position, and all the other saddles will sit further back than that, with the bottom E closest to the rear of the bridge. Different string gauges and variations in string manufacturer's winding methods will give different results per string, there's no "one size fits all" positioning solution.

So to allow this to happen, without the saddles being set so far back that the tensioning spring on the intonation screw isn't fully compressed preventing further movement (you can see in your bridge photo that the bottom E spring is already fairly compressed, so won't move back more than a couple of mm), first adjust the intonation screws so that the saddles are moved forwards just enough so that none of the end of the intonation screws are showing (in reality you only need to do this for the top E saddle as that's where you'll measure for distance), then measure and mark the position for fore/aft alignment. With the neck bolted on, I'd use string or cotton to check the side to side position and mark that. Then with the bridge plate in the correct position, mark where the mounting holes want to go.

With a clear or translucent finish, you could easily then finish the guitar with the screw position marks showing through, then just drill them once the finish is complete. With a solid colour like you're proposing, then you won't see these marks, so you've either got to drill first then plug/cover the holes when wet sanding, or else do all the measuring afterwards. If the latter, then mask up the bridge area before marking the position of it to avoid marking the finish (so easily done even with the best intentions). It's a personal choice, but I think I'd wait until I'd done the finish before making any holes for the bridge or the pickguard.

Swelling and finish cracking from water ingress into holes normally happens along the line of the grain, and as the pickguard holes are close to the edge of the pickguard, even a small crack could be visible on the front and rear edges of the pickguard.

But it's worth just checking the final bridge position now, just to make sure there aren't any clashes with the pickguard. There shouldn't be, but 'measure twice, cut once' always applies.