Even if there is more than one MLS, there’s typically one database which is dominant. In NYC, this is the REBNY RLS. Some agents are members of more than one MLS. When this occurs, the same listing may appear in more than one MLS.
The biggest pitfall of a Flat Fee MLS listing is being listed in the wrong MLS. Some national flat fee listing companies may promise to list your home on “your local MLS” without specifying where your listing will be posted. Oftentimes they end up listing your home on an irrelevant MLS, such as the rarely used New York State MLS in NYC instead of the dominant REBNY RLS broker database.