I know this is an old post but this is a typical issue with all 25-1/2" scale, 22 fret, electric guitars. I've owned a bunch and even the high end ones, with excellent setups, need the Low E string to be stretched way out. A couple of them are maxed out and still ring out a tiny bit sharp, on the 12th fret, while they are perfectly in tune (open). I've seen videos where professional guitar players will mention this same issue. Some going as far as taking that spring completely out, and playing without it, which I don't recommend.
The guitar I currently use the most is the exact same way and its setup is otherwise perfect. The neck is dead straight, it has great action, and a high end Gotoh bridge and Gotoh locking tuners. (It also has a bone nut.) So it's definitely not a quality issue. It's a 2022 model, which I got new, so it's never been tampered with or modded. Just set-up. I also use D’Addario NYXL 09-42 strings, and know when to change them, so there is no issue there.
It's not strings, it's not truss, it's not action, and it's not a hardware issue.
The Number 1 fix is to replace the spring with a shorter one (which is very simple). My guitar still had 3/16" of a gap when the original spring was fully compressed. The saddle only needed another 1/4 turn of the screw to hit intonation, as well, so the saddle still has plenty of room to keep going with the shorter spring in place (not that it needs to).
Also, you shouldn't need to replace the intonation screw since you should have more than enough space to extend the saddle further without the string being near the end of the screw.
The reason this issue happens to many guitars is because they get manufactured in different areas of the world which have different climates and different gravitational pulls (which apparently affect intonation in some way). (Yes, gravity differs, to some degree, depending on where in the world you are.) So, a guitar might have perfect intonation in one area of the world while in a different area will need further adjustment. And with this scale, and this number of frets, the Low E string will already be pretty far extended even if it is keeping intonation.