Brackets don't do anything special in a transliteration, the whole thing is a character class. So:

s//KVTU!BOPUIFS!QFSM!IBDLFS./;y/KQ.!B-JL-PR-Z/JP, a-ik-oq-z/;print
[download]

You can get it warnings-friendly and get a newline printed too doing:

s//KVTU!BOPUIFS!QFSM!IBDLFS./,y/KQ.!B-JL-PR-Z/JP, a-ik-oq-z/,print for
+$/
[download]