Interesting; I'll have to check these out. Up until now the exception I had been aware of was the Dutch flag, which in theory had (16th century) been blue, white, orange, but in practice is flown with blue, white, red.
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I think part of the issue here is distinguishing flags (flown by many people almost all the time) from banners/standards (flown by a small group that can afford to replace them often, only on certain occasions).
So the HRE had a black/gold banner, but when they needed flags, they reached for red/white. (and Muhammad is said to have had a rāya in black but a ʿalam in white; this theory would predict that Muhammad's personal unit would fly the black banner, but his troops in general would have flown white flags)
Then again, maybe black should be added to the basis set (what would this have been? indigo+madder? or after 1500, indigo+cochineal?)
https://www.crwflags.com/fotw/flags/ch-war.html#desc has a chronological list with many pre-1800 blacks, but only two anachronistic choices. (Uri:1291:gold/black, Schaffhausen:1501:green/black, although I should confirm the latter; I'd have expected* gold/black here as well and bet the green is post-Napoleonic) [EDIT: Indeed, now that I read more closely, the colours on the list are indeed post-Napoleonic, and the dates given are only used for sort order. It might be worth looking through some old artwork to see what the pre-1800 colour choices were. EDIT 2: https://de.wikipedia.org/wiki/Schlachtkapelle_Sempach#/media... shows battle flags exactly equivalent to heraldic designs, but was painted ~250 years after the event depicted, so I'm not sure how reliable it may be.]
That having taken care of Prussia, we're left with León and the Mughals. León the city and León the province both use noticeably redder colours than the purpure of the heraldry of León the kingdom, and the Mughal moss green seems to have been more a banner than a flag, flown infrequently enough to use non-lightfast colours: https://en.wikipedia.org/wiki/Flags_of_the_Mughal_Empire#:~:...
Maybe I should say "usually" instead of "fairly reliably", but the exceptions have thus far been reasonably exceptional.
* fun fact: the penis of Bern's bear is hilighted in red, but that of Schaffhausen's ram retains the background gold.