Technically, conventional guitars do not have "perfect" intonation (look it up yourself, it is a rather interesting topic). However, even after carrying out some rudimentary maintenance, the intonation is still quite off on certain notes beyond the 12th fret on my Vintage VS6.
Thus, after some thorough reflection, I am narrowing it down to two possible solutions to fix the problem:
(1) Get a fresh pair of strings (quick and cheap) since the current strings' coating wore off.
(2) Refret the neck (slow, finicky and relatively expensive) since certain frets have become flat after years of playing.
Fingers crossed that the first solution is all I need to solve this. 
I may come back later with an update on this. 
@AmpBenzScientist Thanks for the tips, but I've already tried them without too much success. I still hope it is not a case of refretting, as that would be tedious without paying a lot of money for a qualified luthier.
@Stemist It would be worth the money, I swear that guitars gain character as they age. Even that old American Strat had a golden tone but it was also the unmodified version of what Van Halen used and the same with the Amp. The church also had a Hammond b2. It was a Pentecostal Church so every service was a jam band practice. XD
@AmpBenzScientist I will certainly look into it and see what's available locally if plan A falls flat. Otherwise, I concur with your statements and anecdotes. 👍🏻
@Stemist
Lower your play height and slowly adjust at the bridge. It sounds like the 12th is the point where the deformation to fret is either too much or too little. With the style of guitar pictured, I have little experience outside of semi hollow bodies. I played Super Strats and the knife edge bridge system.
I've also noticed different properties in fret alloys. Some are softer and others are quite tough. I've never had to refret but was able to get away with a light polishing of the frets.