I think the only reason people may see a standard problem with this is because they see it as a web browser first, and as a phone OS second. If it was built as a platform and did not have the capability to view web pages, would anyone complain that they took JS and extended it to offer the local app capabilities they needed?

I think it depends on how you view it. Is it a browser that also happens to power the core of the OS, or is at an OS that also happens to be a browser? I don't think where it came from originally has any bearing in the answer.