Translation:His stomach hurts, I don't know what he ate.
For crying out loud, stop arguing about English, it is the most spoken language in the world so of course ther are going to be variations, its easier for you to learn the duolingo translation and just remember that it can be translated into a synonym than for the volunteer (who is not paid and doing you a heck of a favour) to cater each translation to you´re way of speaking. This is not an omnitool you have to use other resources (by the way, for mandarin, pleco dictionary in the app store...free, totally the best). Every disscusion I go into to see if I can find additional help on grammar and usage of language people are arguing about what other translation should be accepted. It doesn´t work like that.
One more thing, I don´t mean to be disrespectful but "His stomach is very painful".... really? under what circumstances? :p
One of the big reasons that it annoys me that very common ways of expressing in English are not included is for the sake of people doing placement tests.
When I did my placement test I got so many "wrong" simply because Duolingo had only one possible English answer and I couldn't guess it.
Everybody is arguing on English grammar while nobody notices that 肚子 actually means belly and not a specific part of the abdomen. For instance when women have their period they say 肚子疼. I believe it doesn't refer to their stomach. LOL Also used when one is suffering from diarrhea/constipation.
FYI The correct word for stomach is 胃 wèi. 胃疼/胃不舒服 is the correct way to express the discomfort.
It seems that the course admins are going through the dictation exercises like this and updating them to allow 她 and 他 to address the problem you mentioned (which many people have complained about for years) but I don't think they've updated all the exercises yet.
When I'm doing dictation exercises, after I finish typing my answer I always click the button at the bottom to look at the word bank to see which pronoun is the correct one, then switch back and submit my answer.
Native English speakers would never say "his stomach is very painful."
Here are some natural translations: His stomach hurts. His stomach is hurting. His stomach is in pain. His stomach is in a lot of pain. He has a stomachache. He has a pain in his stomach. He has a very bad pain in his stomach. He has a really bad stomachache.
I've never heard anyone say what you are suggesting here in the US.