As of JIRA 4.4 there are dialogs in admin section that rely on decorator=inline parameter so that they don't get admin headers etc. appended. This parameter, when different than admin, is not respected by Studio, which causes the dialogs to have studio admin headers appended.

Additionally, the workflow designer has some special code to remove chrome from JIRA admin pages when it pops up some pages e.g. viewing transitions. The same fix is needed here to enable the fixes on JWD side to work in Studio. andreask will handle the changes required on the workflow designer plugin side.