Unfortunately, keeping it simple doesn't make it right, though it may make it easy.
Ah, but over-complicating something doesn't necessarily make it better, either.
Genius is simplifying the complicated, not complicating the simple, after all.
I'm all for refining our intonation and understand thereof, but this is an area where it is very easy to over-think it, and get lost in the science behind it all.
But if you want really accurate string by string, fret by fret intonation, it's not simple. Because it isn't!
First, it needs to be mentioned that nobody, not even a magician, can ever attain perfect intonation at every string, every fret. Impossible. The only way that could happen is to have an individual fret for each note, and even then, it would only be perfect in one key. As such, everything we do is a compromise. And we must add the various string gauges, and wrap-to-core ratio, type of strings, player's style, players' preferences for certain keys, etc, etc, etc,.... There's no end to the possible scenarios. For example, I promise you that if you hand me your best intonated guitar, that you just tuned with a strobe tuner, I'll play a few things on it, and reach for the headstock and tweak a string or two. It's not that I don't like a perfectly tuned guitar, but rather it's that I am human, and as such, am not perfect, and my left hand's strength has a strange quirk in that my ring and pinky fingers are very strong, and despite years of trying to correct the "problem", I will always sharp certain notes in certain keys. So, depending on which key we're in, I have to tweak the guitar ever so slightly for it to play in perfect tune. Yes, the closer the intonation is to ideal, the less tweaking needs to be done, but fact remains that chasing perfect intonation, which is an impossible goal, is akin to chasing one's tail. As soon as you find an ideal intonation setup for a player who's favorite key is E, you'll have a guitar that will frustrate players whom play in the key of G more often the E, for example.
And then there's the fact that some musicians are more bothered by notes that intonate slightly flat than sharp. And vicey versey; some can't stand a note that plays a tad sharp, but will tolerate a note that is slightly flat. So, for very fussy ears, sometimes we need to move the intonation slight sharp or flat overall, so that it will be more pleasing to the player. Arguing with a seasoned professional musician that your setup is ideal and that he/she needs to get used to hearing "perfection" won't win you many friends, or sales!
And finally, I was much, much, MUCH more concerned with intonation in the first few years I was playing. As I became a better musician, I learned to tune correctly, and stopped blaming the guitar. Yes, it helps that by that time I had attained a very well intonated setup, but no matter if I am playing one of mine, or a client's early 70's Martin with the saddle 1/8" too far forward, I can get 'em to play in tune and just enjoy the music.
After all, making music is the goal of making instruments, right?
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