Thanks for sharing this sequence. I wonder if this isn't obvious somehow, but the blocks of size larger than 1 are not equally distributed. For size 2, it is about twice as likely to not have a repeat,
n = 15; ko =
Prepend[Nest[
Flatten[Partition[#,
2] /. {{2, 2} -> {2, 2, 1, 1}, {2, 1} -> {2, 2, 1}, {1,
2} -> {2, 1, 1}, {1, 1} -> {2, 1}}] &, {2, 2}, n], 1];
Tally[Subsequences[ko, {2}]]
(*{{{1, 2}, 359}, {{2, 2}, 178}, {{2, 1}, 359}, {{1, 1}, 182}}*)
and for size three, the counts are almost the same but some cases are completely missing.
Complement[Tuples[{1, 2}, 3], Subsequences[ko, {3}]]
(*{{1, 1, 1}, {2, 2, 2}}*)
The other thing I am thinking about is what is a good way to code the other definition, starting from self-describing via Split, maybe something involving Table like
Nest[Flatten[Mod[MapIndexed[Table[#2[[1]], #] &, #], 2, 1]] &, {2, 2}, 10]
which seems to have some problem I can't identify.