Actually you CAN run MTO BYPASSING Master planning. Once the sales line is established have a business proces rule to immediately create the Production (Inquire>Production). If the BOM is unique, enter the BOM number in the slaesline subbom first and the MTO Production will respect it.
If you are making subassemblies to the same sales line, be sure to code THOSE BOM lines as line type "Production". When the final Production is updated to "Estimated" or beyond, all subassemby productions will be automatically created (and estimated). Even nicer, the salesline is marked to the production and all sub-poroductions are marked to their parent productions. Using this approach you could set up all MTO items as "do not plan". Of course, if any subasemblies are stocked, they SHOULD be Master Planned (or managed some other way such as Kanban).