I couldn't figure this out either. I believe adding a SRID to a column is currently not supported by MySQL Workbench.
To check that it is indeed not supported, I did the following:
- Added a SRID to a column of an existing DB
- Reversed engineered a script of this DB (using Workbench)
- Checked the script if it included the set SRID for the column
- Was disappointed that it didn't...
The "good" news is though, that as it is not supported, MySQL Workbench won't pick up on a missing SRID on a column when synchronizing sources.
This means that once you set the SRID on a column yourself, it won't cause any problems when synchronizing in the futures.
Note that in order to set a SRID on a column, there can't be a (spatial) index on that column. Therefore, you must remove the index, set the SRID and then add the index back.
Below is a short and simple script, which I used to do this. Don't forget to update it to your use-case:
DROP INDEX `my_idx` ON my_table;
ALTER TABLE my_table MODIFY COLUMN my_column POINT NOT NULL SRID 4326;
ALTER TABLE my_table ADD SPATIAL INDEX `my_idx` (`my_column`) VISIBLE;