The podcast only feed is ideal for submitting to podcasting directories and iTunes because it only contains blog posts with media associated with them. When you have your items per feed setting for your blog set at 20, and the last 20 blog posts you made, only 5 of them have episodes, then your main RSS feed in iTunes will only show 5 episodes (because iTunes doesn't show posts without media). If you use the podcast only feed, iTunes would still display your latest 20 episodes, because the podcast only feed does not include blog posts.
The example above presumes you have created more than 20 podcast episodes and also that you also blog (write posts without media). If you only ever create podcast episodes on your WordPress site, then the main RSS feed will be identical to your podcast only feed and you can ignore the note.
The note is there to help new podcasters decide which feed is best to submit to iTunes.