I've watched through all 8 Tenchi in Tokyo DVDs 
about 4 times since I've bought them, and I have 
never seen Sakuya in military dress.

Have you seen those Ryoko cels with the Tenchi in 
Tokyo eyes, but she's wearing a hood   trenchcoat 
and has binoculars?  I haven't seen this either 
in the series, BUT I have seen the Tenchi in 
Tokyo japanese commercial (an extra on one of the 
discs and on disc3 of the tenchi ova) that has 
the girls dressed up in trenchcoats (for one part 
of the commercial.)

So, the original cel in question could have been 
only used in a commercial and/or an outtake.

Or Pioneer screwed up big time and left out an 
episode, but that's highly unlikely.