After you transmuted your starter set based on the Krytan armor set’s appearance, you can now transmute your new set based on the starter’s set appearance (which it should have inherited from the Krytan one).
If that doesn’t work, that’s a bug, and I’d contact ArenaNet.
Yes I tried this, even tried putting the Krytan armor on the left or right side, and there both obviously medium set it’s not like I’m trying to cross it, and the button to confirm just stays greyed out.
does not matter which side either armor piece is. the transmute is greyed out until you choose which options to merge into your new armor piece.
e.g. the top option will be the “look” – you would choose your old krytan look, the next option down is the main armor stats – choose the new upgraded piece.. the last option is the upgrades (if any)