I did it in that order - eVisa first, then included the TRN from the application in the exemption. Exemption came through after 4 days, eVisa still pending.
It doesn't seem to matter but having the exemption should have pushed them to issue the eVisa as by all accounts. Unless you have an exemption you shouldn't have been issued an eVisa or you are put to the back of the pile but that doesn't seem to be the case.