This encoding already goes too far towards “support the existing flags”.
As a simple example, look at the pattern of the flag of the Comoros (https://en.wikipedia.org/wiki/Flag_of_the_Comoros). Even using just the top colours (FTA: “red, then white, blue, yellow/gold, green, black and orange”), there already are 7 × 6 × 5 × 5 × 5 = 5,250 ways to colour it so that no two neighbouring colour bands are identical. That alone doesn’t fit into 12 bits.
Even limiting one to all colours different, there still are 7 × 6 × 5 × 4 × 3 = 2,520 colourings using the 7 most popular colours. That’s (just) over 11 bits.
And then, you still have to encode the crescent with the four stars.
We could also complain that the crescent is a complex primitive. Why not define it with three parameters: two circle radii with a center offset?
Choosing the primitives is hard and requires domain knowledge/taste, and finding a simple enough implementation solving for key usecases (e.g. decent coverage of maps, meaningful bit encoding) and descoping (e.g. deciding on no emblems) is also hard.
But I am personally impressed with the primitives the author created and the scope simplifications done to achieve it.