It doesn't look like it's anything to do with the API, it's to do with whether the user has the "bot" flag. An upload via Special:Upload from a bot-flagged account is flagged as bot too. It looks like the same happens with any logged action.

 

That would be nice. But it looks like the code that does this flagging is buried deep without taking parameters to actually control it, so adding the option to the API in a non-hacky way doesn't seem easy.

OTOH, if you ignore the warning the API will generate about an unused parameter, you could just pass "&bot=0" to the API action=upload call.