There was some discussion on another forum about what key signature to use when you were notating e.g. a Scottish pipe tune in a modal scale with flattened 7ths. i.e. in the key of A all Gs would be naturals, therefore some people would only put 2 #s in the key signature.

To me, having laboriously and faithfully learned standard music theory nearly 60 years ago, this was confusing and "wrong" (dare I say it?), and would suggest the key was either D or Bm. My take on it was that you should still use the usual A key sig of 3 #s and then write a natural in front of each G in the score:


That's counterproductive for diatonic instruments. It tells a moothie player to pick up the wrong instrument and tells a clarsach player to use the wrong lever settings. It also gives a singer the wrong idea entirely of what pitch set they'll be using.

"Standard" music theory was never as rigid as you make out. Bach never notated a piece in G minor with two flats. Correct modal notation for Scottish music predates the modern convention for minor key signatures and has been in continuous use for more than 300 years.

For more complex modal systems like Turkish or Indian classical music, all the players know exactly what set of pitches they'll be using (and when, if the mode has to modulate). This tells them how to set the instrument up (if it's something like a kanun or a wire harp), what fingerboard positions will be in play (if it's a ud or violin), which pitch of flute to choose and which notes in its scale will need which sort of inflection... The performance will usually open with a semi-improvisatory prelude (taksim, alap) whose main point is to get everybody perfectly in tune across the whole range of the mode, and for each of the standard cadential figures. Misinformation of the sort you're advocating about where the tonal centre is and what the pitches to be used will be would bring the entire performance to a grinding halt before it even started.

If you play any instrument with sizable differences in the technique required for different keys, you will think the same way. If I'm playing the recorder in a key with a bunch of accidentals, I'll quietly tell my fingers which ones will be needed to do the cross fingerings. If you play a chromatic button accordion, you have three different alternative fingering patterns each of which deals with four keys, and you'll be using different ones if you think the primary key is A than if you think it's D.

(or if there had to be any compromise it would be to write the key sig as F#, C#, Gnat [...])

That was once common in pipe music, David Glen used it a lot.