Trying to get to the "bottom" of this

Since he recovered. . Maybe he just picked up the habit. . I wouldn't worry

 

I hate to be the one to break this to you, but all chickens squat when they poop.

That's how you can tell a chicken is getting ready to poop, in case you happen to be holding it on your lap. When they lower their derriere, that's the "tell" and you can avoid getting nailed if you place the chicken on the ground as quickly as you can.

Granted, some squat lower than others, but they all squat.

Were you under the impression that boy chickens stand up to go?

 

I second this. All chickens squat to poop! Some of them will even back up a pace or two, wiggle their tail feathers, and then squat slightly to poop. This is a telltale sign to get them off of your lap! They do it from being chicks to full grown hens and roosters.

There is no reason not to breed him! Chicks can get pasty butt (or several other issues) that result in perfectly normal irritation or inflammation on their rears. This shouldn't affect their breeding potential and he sounds like a fine rooster.