The funny thing is, the reason, according to Ubisoft why the game has no progression for the co-op partner, only the host, so they can "experience their own unique journey".
Good lord that's a stupid reason.
Getting knocked out is annoying, extremely so as you can't avoid it anyway, you hit that cap and YOU WILL get kidnapped no matter what.
As a free roam game, just derping around, especially so with a friend is actually really fun, but good lord does the game want you to not do that.
If i remember correctly, depending on your choices you can recruit the characters to come with you in the next chapters, so you can use your hard work again.