Merkle tree H(RBIT(X) ⊕ Y) instead of H(X || Y)
The problems mentioned in Can XOR be used in a Merkle Tree instead of concatenation? are just special cases of a fundamental problem: the construction is not second-preimage resistant. In fact, it is even worse in the sense that you can find a preimage with any $X$ value you like (similarly any $Y$ value you like).

You can open a Merkle-tree node $H( X \oplus Y)$ to any other values $X'$ and $Y'$ as long as $X \oplus Y = X' \oplus Y'$. If you can do this, then you can open a Merkle-tree leaf to literally any value. Flipping/inverting some bits (and indeed, any linear operation) won't make this attack any harder.