#1
Is it bad that I have to get my intonation right and it doesn't end up in a 3 x 2 slope like most guitars are set up?

It even seems like sometimes I don't have enough backspace to intonate a string correctly.
#3
A picture that clearly shows the issue you're having might help.

I always assumed saddles being as you've described were only done just to look good in a picture and the guitar probably hasn't had a proper setup. Unless the guitar miraculously had perfect intonation right out of the factory.

Some more info might help as well. What string gauges? Tuning? Scale? How's your action? I don't know if any of that matters, but when I struggle to get proper intonation, I check other things. Sometimes lowering the culprit saddle a little seems to help.

I also noticed proper intonation was more achievable when I got rid of the huge ass strings on my 25.5" 7 string. Or maybe I'm just an idiot and that didn't help at all.
Ibanez Prestige RG852MPB
Ibanez Prestige RG652KFX
ESP E-II M-1
LTD AW-7
Schecter Loomis NT
EVH 5150 III 50
PRS 212 DB
Line 6 POD HD500X
Deadhorse OD/Boss HM-2
#4
Strat style guitar
25.5" scale
I set the neck relief as well as I can on the truss rod.

11 gauge Ernie Ball Power Slinky