Ledo rushed to Kugel, because it was a soothing and easy choice. He was just escaping most of his internal strugles and it felt easy to go back to being an underdog.
He even stated he's not able to be a leader, and it's true he doesn't seem like he possesses the traits at his young age.
But it seems obvious he won't blindly acknowledge orders, even more so when he's ordered to kill people from Gargantia...
He also felt the "happiness" definition from the alliance he a lot different from the one he felt in Gargantia, another way that felt efficient and good against all odds and appearances.

Regarding body fluids and grooming, well I guess the suits and the seats do what's necessary... After all, that matter vaporising laser probably also works there and even converts those excretions into energy/simple matter or whatever needed for life support.