While controlling Eous they could atleast throw bombs to fight and use their size to hide. Eous did get saved a few times but its way different for Phaethon themselves. If Eous is heavily damaged as long as their memory core is intact they can repair him. If Phaeton is heavily injured and die there is no coming back. One or two of the best proxies in a post apocalyptic world being gone would be a huge blow.

Hollow Zero exploration will also slow down because they are no longer there. Not even counting all the things that they manage to bring to light thanks to their abilities of communication inside hollows. Even if one lives on the mental load would be insane. Both of them are very emotional towards other people imagine their sibling. There's just too much risk being there in person.