• Summary / Title: Pirate Fleet cannot attack Ally 
• Description: I cannot invade the system.
• Steps to Reproduce: load file. check for Bundus
• Reproducibility: 5/5
• Expected Behavior: To be able to invade a system with my privateer fleet.
• Notes:  I changed my fleet to privateers at Rhea. Can you still attack if AI sees you change to privateers?
• Save:  AutoSave 4632.sav
  

Apparently the fact I cannot invade it is because all other major factions have alliance with pirates. Is this intended? I will try to kill all pirates and then see what happen.

Most likely you still will not be able to invade, because relations status isn't reset when Pirate League is destroyed. As this option is available from beginning of the game, I assume it is oriented towards early usage.