Thanks for the detailed write-up! I don’t really consider this a huge issue since the guitar actually plays wonderfully, but I’m a tinkerer and this sounds like a fun challenge. Have you tried this approach before, and would you say that this technique helped?The saddles do indeed look odd. Sometimes funky angles happen, but those angles combine with the notched saddles to make the string spacing seriously off, to the point that I would consider the guitar unplayable.
If that were my guitar, I would start over from scratch. First I'd try to get the saddles more parallel, even to the point of having no radius to speak of, and push them as close together as possible. Then I'd set the height of the high and low E strings with the saddles flat/parallel to the bridge plate. Then I'd raise the D/G saddle much too high in order to get it out of the way, and use an under-string radius gauge to set the height of the A and B strings. Then drop the D/G saddle down, preferably as close to parallel to the plate as you can get it without completely disregarding what the radius gauge is telling you. See where the intonation needs to be from there; you may be surprised. (Alternate method: start by setting the heights of the D and G strings, compromising slightly by trying to keep the saddle parallel to the bridge plate)
The fact that you have consistent string height now is irrelevant when the string spacing is that wrong. It needs to be fixed.
The way that those saddles are constructed suggests that the string spacing might be better with a flatter radius. Sometimes a saddle radius flatter than the radius of the board works; it's worth a try. (That's a hotly debated issue, btw!)