MariaDB has been diverging from MySQL for some time and now they are in fact so different they are not-compatible.
In Zabbix codebase they are treated the same what introduces many problems to development.
One example is divergent error codes:
4031 means ER_CLIENT_INTERACTION_TIMEOUT in MySQL and ER_REFERENCED_TRG_DOES_NOT_EXIST in MariaDB.

To separate them we would need to:
1) add separate ./configure option:

 --with-mariadb

and make

--with-mysql 

explicitly incompatible with MariaDB.

2) provide separate packages - mysql and mariadb and docker containers etc.

3) add checks to DB connections so that zabbix compiled with MariaDB connectors refuses to work with MySQL and vice-versa. (there is proposal to allow this if AllowUnsupportedDBVersions=1)