This sort of ties in with an earlier suggestion that Supreme Commander Leonard was replaced by the Robotech Masters BEFORE the start of the 2RW*. Now most people I think when viewing Zor Prime's flashbacks and the viewing of ASC issue items (armor, clothing, etc) assume one of two basic positions:

-Animation "Glitch" related to RT's origins and should be ignored

-his mental state was really messed up and images where overlapping/substituted for more familiar/recent designs.

Here is another thought though. What if Zor Prime (and possibly more than just these two) was used previously to collect first hand intelligence BEFORE the formal start of the 2RW and the attack on the Moon Base also had the unstated objective of retrieving him? The Red Bioroid IINM is absent from that particular battle (owning to RT's use of recycled footage for Ep.37) and this could be an explanation for his lack of appearance.

It would certainly explain Zor's Flashback sequences visually. If he was inserted like the Zentraedi Spies, maybe he (and his team) assumed the roles of facility personnel. Given that it's likely a large base, they would be able to proceed unnoticed for the most part (much like the Spies did).

We know the Masters could land decent sized vessels on Earth ("Half-Moon") undetected and one is left with the impression that the Masters did some intelligence gathering before the start of the 2RW when they briefed the Elders. Weather the insertion was at the Moon Base (a bit more challenging) than on Earth (easily doable given "Half-Moon) is debatable if it happened.

It should be pointed out the Masters voyage was to take 15years and they launched a few episodes BEFORE the SDF-1 was destroyed and Ep.37 is said to take place 15years exactly after Ep.36. Depending on the specifics of the 15year voyage for the Masters (exact or approximate), this gives them an opportunity to have done this.

*Link on this topic is here: http://rdfhqcommunicationscenter.yuku.com/topic/467