Honestly, sounds like you are talking about multiple things.................
"Is one trait of a higher end guitar that all the frets are in tune when the strings are tuned?" = well, if the guitar is intonated correct, then all the frets are properly tuned when you tune it. Easy quick and dirty check, tune your guitar, then check the tuning at the 12th fret, all the strings should read the same as their open counterpart, but thats ANY guitar, a $1000 or a $199 all get the same basic set up
" I play along fine with Griff by myself. Every time I'm in a jam session every note I play seems out of tune" = I think, and I am guessing, what it is here is the difference to playing with a jam track vs live, a jam track it stays the same, its consistent, your ear knows what it needs to hear. At a jam, people are playing different things that compliment each other, and it throws many people off, maybe the drummer throws in a fill you are not expecting and suddenly you miss a barre
A suggestion, if working in the key of A, go to youtube and find every jam track, and play over them, all the different timings, rhythms, everything, it will help to get used to things on the fly, and of course, practice your canned solos until you can order Chinese food while playing it