Ok, I think the ref's going to have to call this a fair play. It appears to be freeing _all_ of its mkII stuff, and then all its mkIII, and then all its mkIV, and finally freeing some (possibly all) of it's mkV stuff. I think the low low-mark population is due to the AI only holding 33 planets, the high-difficulty increasing the mark level of a fair number of those, and the fairly intense nerfing/neutering/cleanup that's taken place here and there.
On the bright side, if you counterattack fairly soon (before a lot of reinforcements), there won't be so many guards to deal with.
Btw, I was wrong about it just creating ships to fill in the gaps, it doesn't appear to do anything like that. If there were any barracks it would pull from those, but it genuinely had those ships to begin with.