creating an application ACE is not hard (if you can live with
numeric data):
$ SET FILE/ACL=(app,flags=%x81,size={8+4*{#longwords}},-
	data={longword1},{longword2}...)
Apparently one can specify an ACE the same way as DIRECTORY/ACL
displays it - I wonder if that's documented anywhere.

An example (with GCYB flag):
$set file/acl=(app,flags=3,size=16,data=%X42594347,%x0fedcba90) jnk.tmp

creates an ace of appropriate size with the data.
(got the value via 
cvs=f$cvsi(0,32,"GCYB")
)