Yesterday jessehs was writing the filter formats plugin and we had a discussion live and then on IRC with marvil07 whether we should migrate the filter format table and then run a migration for each format to bring the filters over or just add the filter list to the formats in prepareRow. We are doing the latter.
Noone suggests bringing over entities and then fields separately either.
SQL can not store arrays but we are not architecturing based on SQL limitations. We will go with whatever is right and not with what SQL enforces. It is the duty of the SQL source plugins to code around these limitations. For example, the permissions on a role are stored as a comma separated string and the source plugin will make an array out of that.
To sum up: we are not writing a source plugin per SQL table but per object.