Hi Boris, I haven't had either running under 5.4. I'm guessing by 5.4 you really mean 5.4/jquery?
Im guessing tapestry-atmosphere would work with 5.4/prototype. I think there's a single line of js that relies on prototype's json utils which will need to be tweaked to the jquery equivalent. tapestry-cometd should work as is under 5.4/jquery.