Just realised that this question still has no accepted answer. So, to answer it myself...
No - Fantom does not support JSR-223. (As of 15 May 2015.)
There have been no further comments on the Fantom blog (re http://fantom.org/forum/topic/2127 or otherwise). There appears to be nothing on the interweb re 'Fantom', 'javax.script' and 'JSR-223' as far as an implementation for Fantom goes.