OGS used to have only one rating, which carried over to the present day as Overall, and there has been no change to how it is calculated afaik. The time-class based ratings have been described as 'experiment' by the developers.
The fact 13x13 and 9x9 games have always been a part of our rating might imply that the importance placed on these sizes was a part of the plan to build the initial OGS character/differentiator, which may have a lot to do with the reputation that OGS is the Go server for beginners.
Now that OGS has been successful to the point it is the largest Go server outside of China/Korea/Japan, it may be time to reconsider this in order to attract stronger players at the expense of possibly alienating some 9x9 only and 13x13 only players.
Single/multi rating issue might be less important to this critical decision for OGS to grow further.