Keep in mind that support.checkClone is not only for old Webkit. It currently and should continue to be false for IE6/7
IE6/7 problem is with defaultChecked attribute, if it set to true then cloned radio will be checked, and you already have fix for IE, which is not involve checkClone property. But because checkClone is false for IE6/7 you run some needless operations, that can be avoided.
Does removing the second cloneNode call have any adverse effects for other browsers?
I did not find any. But i'm concern about this ticket description -- http://bugs.jquery.com/ticket/5929
I have found problems only with radio input, not with checkbox input.
Btw link that i was mentioned in other ticket have illustrated some others bugs -- http://jsfiddle.net/fxT2r/.
But i suppose its a very edge cases?