Upgrading your organization from current versions to Exchange Server SE

So, am I correct in my interpretation?  If a client obtains all E3 or E5 licenses for their users, they are properly licensed for Exchange SE?

If that's correct, that's great... how do we convert existing Apps for Enterprise licenses to E3 licenses without losing the remaining 8-month investment in the prepaid Apps for Enterprise licenses we currently have?  Since Microsoft went with the "New Customer Experience" (Everyone I know is still laughing about that... and cursing Microsoft for it), I don't see a clear path to properly license Exchange SE without either staying on an unsupported version, being out of compliance, or unnecessarily (though intentional by MS?) overspending on Microsoft licenses.  Am I missing something?