Well, in terms of maintenance it's a little bit more work.

Sure, it has the features and reliability. But does that really justify having to maintain a completely new environment? Maybe it does, maybe it doesn't; it depends.

No you may not be embedding it in your app, but it's now a part of your stack. You'll need to keep an eye on updates, etc for a completely different environment.

Plus there are other factors, like approved languages. Certain companies only allow using languages X and Y. Don't even think about language Z. I had to re-write an 80loc Python script to a much larger Perl one because I just didn't grok Perl all too well at the time. It didn't matter that Python was installed on the system. All that mattered was that Perl was approved and Python was not.