I never used Apple's Mail server myself - I use Kerio Connect, but I believe what happened was that the originally included webmail i.e. RoundCube used MySQL which Apple used to include with their server software. Apple stopped including MySQL and this I believe was the reason for stopping the inclusion of RoundCube which required MySQL.
I believe the TopicDesk installer therefore also installs a version of MySQL to allow their software to function.
This possibly relates to licensing terms, similarly Apple stopped using SAMBA for SMB support due to a change in the SAMBA licensing terms, and MySQL which is now owned by Oracle may have also moved to licensing terms Apple were unhappy with.
Note: If as I believe TopicDesk are installing their own copy of MySQL then it is they who have to adhere to any MySQL licensing terms rather than Apple.
What is perhaps disappointing is that Apple could have in theory switched to using Marimba instead of MySQL. Marimba was written as a 100% compatible replacement for MySQL by people also unhappy with Oracle's control over MySQL.
Apple use PostgreSQL as the database software for their Wiki and Profile Manager.