We use them because they're there. Generally, for good practice, we try to use the Joomla libraries where possible. In some cases (certainly not all), they wrap around standard PHP functionality and give enhanced compatibility across different types of servers/configurations (windows, linux, etc).
We just uploaded 2.5.3. That was the ONLY change, so don't feel like you need to get it if your running now. We're hoping to ride this one a little longer than 1 day. If there's no more issues, we can get back to feature improvements
Thanks a ton for all your feedback!