They answer two different questions: Done is a decision you make, while read is simply a record of what you have opened.
Marking as Done says there is nothing more to do with a message. It is listed in the Done column of the Later Board and marked read, while staying in your inbox. You can set it Undone at any time to clear the status.
If you want a message out of sight until later, that is Reply Later instead: a snoozed email does leave the list until its time comes round.
Read and unread happen on their own. Opening an email marks it read, which tracks what you have seen rather than what you have finished with. An email can easily be read and still need an answer, which is exactly the gap Done fills.
Both are easy to work with in the mail list. The Filters in the account picker are All, Unread and Starred, so the Unread filter narrows the list to mail you have not opened yet.
