He'll be fine. I'm not a fan of most of the "in the wild" analogies, but you're spot on. It's not like they survived eating off of sterile plastic plates for thousands of years before us. Just think of it as a bit of extra fiber in his diet!

Just like you learned, most ball pythons are simply more comfortable eating in their own enclosures. There aren't many reasons (good ones anyway) to take them out of their comfort zone during feeding time. I wouldn't mess with the separate tub next time if I were you.