Everything you describe is exactly what happens with 7/64" at the 12th. The G & Low E tend to be the issue. Pete & I pulled the springs out of his Strat and it helped some. He loves him some high action. I personally don't like the tonality, intonation and spongy-wierdness when you get above the 17th. If you're at 0.030" at the 1st fret, that means you're almost at 0.250 at the 22nd. In what universe is a note in tune when a string is lengthened to that degree (when fretted).
Also...get some calipers at the Ace hardware for $15.00, or the string gauge from Stewmac. When you get to measuring this stuff regularly, and then you look at the Irwin guitars, Moriarty guitars, Scarlet-Fire guitars...you'll see...They're just isn't 1/4" of freeboard at the 22-24th fret! Tiger & Rosebud (I believe) have something like a 1.5 degree neck angle. Almost flat. Not much more than a stock Strat. You're eye won't lie to you.
I like my Strat set up with about 0.025-0.030" neck relief. I do my own fret work, and I also like to push the action threshold upward. Fender recommendations are all over the place, just like their setup work. Most players want the strings on the deck. 0.012 is not uncommon. So the Gary Brawer setting of 0.030" is just fine. I prefer the action set to 5/64" to 3/32". It helps de-spongify the upper frets, and bring the G & E intonation to within 3-5 cents with a Peterson Strobe (and GTR temperment). Your personal fret work can wonk this a bit.
"Hi Ho...the Carrion Crow...FoldeRoldeRiddle"