As stated in RFC8032 and FIPS 186-5, Ed25519 signatures uses the following encoding method:
A curve point (x,y), with coordinates in the range 0 <= x,y < p, is coded as follows. First, encode the y-coordinate as a little-endian string of 32 octets. The most significant bit of the final octet is always zero. To form the encoding of the point, copy the least significant bit of the x-coordinate to the most significant bit of the final octet.
Is there any benefit to encode the y-coordinate rather than the x-coordinate here?
My question comes from the fact that the SEC standard encodes x-coordinates, so it would have been less confusing to follow the same approach in my opinion.