Spoiler Alert - Click to Toggle
The main bad guy crash landed on the planet. He did not figure all that stuff out on his own because it's said that there was lots of alien stuff there (like the ships that they use) and also part of the weapon he was so lustful for. The previous aliens shot half of it into space. As to why he looks alien, to me it was inferred that was a side-effect of using the life machine with other aliens' DNA mixing in with his. The life machine was already there with all of the other war tech, by the way. Once he started sucking up actual humans again, he started to get some human looks back.
The aliens weren't affected by Mars Attacks-style vulnerability. In Mars Attacks their brains exploded from how shitty the music is. By the way there were absolutely ZERO comedic payoffs in Mars Attacks. That movie is seriously more boring than a four hour long MP3 of complete silence that you encoded at 320kbps for maximum quality and listening for flaws in the encoding. I've tried twice to make it through that movie. Can't do it. Anyway in Star Trek it was just VHF frequencies that caused the ships to lose communication with each other. The rest of the universe had switched to ATSC by this time and no longer used VHF so the aliens who designed the ships didn't think that would be a problem. They probably didn't even need a song playing.
The bad guy didn't know the albino alien girl was hiding his old starship because frankly he had no reason to care. As far as he was concerned, the ship was a wreck. He found sweet new shit to keep his attention. He knew that ship could not possibly be a threat. He didn't forget about it but he clearly had no reason to care. He seemed pretty surprised when he saw it again.