I would be delighted to learn that I'm wrong or out-of-date on this issue, but it seems to me that it is still the case that custom WYSIWYG fields (for posts, pages or custom post types) don't have fully-functioning 'insert media' capabilities, especially in cases where you've opted to not include the standard WP content editor field. One can include the media uploader and icons with media_buttons => true, but the 'Insert into' button doesn't appear, or doesn't insert images into the custom field.
In running through the use cases in my head, I have to admit that using the standard WP editor field is probably okay in most of them. But I also know that it's suboptimal when you are really trying to craft a clear workflow for specific clients - one of the great things about WP is the ability to make a CMS that works the way the client thinks, not the other way around. There are many cases where one might need multiple fields with inline image capability, or simply want to contextualize the WYSIWYG field with a label, description or grouped with fields that share a common theme (Event Details, eg).
As this isn't a deal-breaker by any means, I imagine this is a feature request - and in the meantime, perhaps a clarification in the Codex would be helpful, specifying that media_buttons for custom fields won't work as one might expect.