Possible internal contamination from soaking or scalding slaughtered chicken in hot water to ease plucking
Are you looking to do this for industrial purposes? Or are you just doing this at home? Also, what is your major concern - putrid water getting into the lungs and growing from there? The water should be hot enough to kill most bacteria at boiling after a relatively short exposure (anything from defecation or exposed on the feathers).

As for internal temperature, at a small home scale, I don't think it's that big of a deal. Whenever we slaughtered our chickens we always scalded them to remove the feathers, and never had any issue. Same with the hogs (removing hair).

Anything which may get kicked off internally should be halted/paused relatively quickly by proper sanitation and food prep techniques after plucking. If you are cooking the bird right away, you shouldn't have any issue because it would take awhile at room temperature for most bacteria to really start working their mojo. Assuming you slaughter, scald, defeather, clean, and then do whatever butchering is necessary (if any), you're talking about an hour to an hour and a half (generously). Afterwards, it'll go in a freezer or a refrigerator (both of which will slow the metabolism of any bacteria), or a pan (which will kill the bacteria using proper cooking techniques). There simply shouldn't be enough time IMHO. Now, I wouldn't let the bird sit around for a few hours, but that's pretty common sense.