But, if you are using a tuning for which the "octave" isn't 1200 cents, but something else, it still uses a 1200 cent octave, but should use the "formal octave" from that scale instead.

Pianoteq already has this built in to some degree when it reads scala files. For instance, if you load the Bohlen-Pierce scale into Pianoteq, it correctly notes that the "octave" in this scale - aka the interval of equivalence - is now 1901.955 cents or 3/1 (aka the "tritave" rather than the octave). This is just the last line of the Scala file - if the last line is 1200 cents, it will say that's the interval of equivalence; if it's 1901.955 cents, it'll say that, etc.

So when you go to the adjacent channels, it should simply use that possibly-non-octave interval of equivalence it's already parsing from the Scala file, rather than hard-coding it to 1200 cents.