There are other things you've said before your questions I want to address first...
Separate media links on blog from becoming a podcast (enclosures in your feed): Many versions of WordPress ago, I believe 2.5, WordPress developers decided to add a feature that would automatically create media links in blog posts into enclosures in the feed. You need a plugin to turn this behavior back off. A podcasting plugin such as PowerPress will automatically do this, as you can imagine this behavior can be a real headache if your doing a podcast where you reference other media. If you decide to roll with a different plugin other than for podcasting, just keep in mind you will need to find a plugin that will disable the auto enclosure feature built into WordPress.
Question 1: You can turn off the option to enhance your blog feeds, at that point it does not add any overhead to your current feeds, and only adds a unique podcast feed that you can just never use. This is the same feed you're accustomed with with PodPress. We originally created PowerPress to be a fork of PodPress, but within 2 weeks we decided to write our own podcast plugin from scratch, we designed PowerPress from the beginning to replace PodPress since we were all using that plugin back in 2008 when PodPress was essentially abandoned.
Question 2: Blubrry statistics are based on the file name itself, as long as each file name is unique, then they will be counted separately. This gives you the freedom to move the files from one CDN to another, so as long as you don't rename the file name you're good to go. You definitely want to use Blubrry statistics since it breaks down downloads by platform, client, etc... which tells you a lot more about the consumption of the media than any web stats or counter provided in PodPress will report.
If you are creating some of this media yourself though, I would highly suggest that you come up with a podcasting strategy. Your missing out on getting your content consumed in a lot of other places including iTunes, Zune marketplace, Blubrry.com, Miro, Android podcast apps, on Samsung SmartTVs, etc... iTunes alone will usually account for 50-80% alone of media downloads, there's real value being there.