it is correct that iTunes shows only one media file per post regardless how many media files are attached to the post. I'm not entirely sure why this is how it is. But the RSS specification is not clear about the question how many files (
<enclosures>) per post are allowed. Since this is a fundamentally problem, you can most likely not change this behaviour of iTunes.
One solution is maybe to post part1 in a post with a full description of the episode content and to post the second part in a further post which contains only a reference to the first part. You could hide the posts with the second part on the blog page with plugins or maybe some code.
Or you create posts and attach both parts and also create additional posts with the second part. If you hide the posts with the second part on the blog page then only the posts with both parts will be visible on the blog. But both posts will be in the feed.
This is not ideal. But maybe good enough. You could of course create and register a second feed (maybe a category feed or a podPress Feed with active category filter) with posts which contain the second parts. But this solution would have a big disadvantage that the listeners would have to subscribe to two different feeds and the episodes would not be in the same column in the iTunes client software. It is maybe a little bit to complicated or inconvenient for some listeners.
Why do you have 2 parts? Are the episodes to big to have only file?
Maybe you could offer two feeds one with high quality files and one with audio files with a lower quality and size. If the files of different file types (e.g. .m4a and .mp3) then you could attach both versions of an episode to one post and use the filter type filter of the podPress Feeds to create two RSS feeds.