XWIKI-10405 we've introduced a new mail API (replacing the old mailsender plugin). While doing so we introduced new mail configuration properties in xwiki.properties but we kept using the old mail configuration located in XWikiPreferences.
XWIKI-11541 we've moved all email configurations found in XWikiPreferences into Mail.MailConfig by introducing a mail UI module. While doing so, we decided to keep the old XWikiPreferences mail properties but deprecate them and retire them after one full cycle (i.e. in 8.0M1).