One house rule that I always like to use Any ships on bystander colonies can also be used to ally in an encounter taking place with the planet they occupy if they are invited. This is in addition to any ships sent from elsewhere for the purposes of allying in the usual way.
This means that you can ally with more than four ships when you have a bystander colony on an encountered planet. For example, In allying with the defense, you send four ships from various other colonies, plus you can decide to include two ships on a bystander colony on that planet). If you aren't careful when doing this, you might lose a colony that wasn't otherwise at risk. It just makes sense thematically because those ships are already over there, and it can add some interesting high stakes elements to encounters.
Now that the Filth are in the game, I would expect this option to be used much more frequently.