Yes this is expected, because MySQL Workbench is an Oracle product and it does not officially support MariaDB which is actually a MySQL competitor. Workbench is warning you about potential incompatibilities, not necessarily detected ones. In most cases, it can be safely ignored.
The MariaDB knowledge-base article on MySQL compatibility describes the relationship best (emphasis mine):
For all practical purposes, MariaDB is a binary drop in replacement of the same MySQL version (for example MySQL 5.1 -> MariaDB 5.1, MariaDB 5.2 & MariaDB 5.3 are compatible. MySQL 5.5 is compatible with MariaDB 5.5 and also in practice with MariaDB 10.0). What this means is that:
- Data and table definition files (.frm) files are binary compatible.
- See note below for an incompatibility with views!
- All client APIs, protocols and structs are identical.
All filenames, binaries, paths, ports, sockets, and etc... should be the same.
- All MySQL connectors (PHP, Perl, Python, Java, .NET, MyODBC, Ruby, MySQL C connector etc) work unchanged with MariaDB.
- There are some installation issues with PHP5 that you should be aware of (a bug in how the old PHP5 client checks library compatibility).
- The mysql-client package also works with MariaDB server.
- The shared client library is binary compatible with MySQL's client library.
This means that for most cases, you can just uninstall MySQL and install MariaDB and you are good to go. (No need to convert any datafiles if you use same main version, like 5.1). You must however still run mysql_upgrade to finish the upgrade. This is needed to ensure that your mysql privilege and event tables are updated with the new fields MariaDB uses.
We do monthly merges with the MySQL code base to ensure we keep up our compatibility and get any and all features and bug fixes Oracle adds.
All that being said, there are some incompatibilities that may or may not affect you. The linked KB article has a section on known incompatibilities between different versions of MySQL and MariaDB. Refer to the section for your MariaDB version for notes that may affect you.