Some remarks about drop-down lists (HTML <select>s) in "Structure > Relation view" mode:
1. Every <option> (column's full name) starts with the name of current database - is it required? For MySQL, not.
2. It would be more user-friendly to show table/column hierarchy in lists by HTML tag <optgroup>, than by using syntax "db_name.table_name.column_name".
About (1), the idea was that some day we could reference a field from another database. There was another reason, I'll check in the code.
About (2), do you have time to prepare a patch?
Yes, I'll try.
This area was improved with https://github.com/phpmyadmin/phpmyadmin/pull/438