In the case of (1) the biggest issue I see is when people from an organization leave. It'll be interesting to see how Google handles that in Google+ for Apps users.
As an example, right now, when deleting a Google Apps account all of the user's shared docs, calendars, emails, etc. are deleted. I'm not sure if there's a way to preserve information or transition ownership easily.
For organizations like schools I could easily envision someone wanting to take their Google+ content with them once they graduate. For companies there's usually a mix of content that should be removed and preserved that's specific to that organization.
For my personal domain I do want Google Apps features to have parity with GMail. It's not that I don't understand the difference. It's that I don't want to split my information between multiple online identities.