I'm about to start playing this mod again tomorrow. I can give it a try and report back to you.

I have been playing this mod for quite some time and noticed the same thing. It is pretty annoying to have undefended planets and stations. While you can put garrisons there yourself that is very expensive and time consuming.

My generals seem to fill up the Garrisons just fine. Which faction are you fighting, anyway? Empire, Hutts, or Rebels?

I hate Rebels, but I also hate fleshlings, so I went to war against the Rebels first, before declaring war on the Hutts and Empire after securing enough planets. :^)