No that is just an alternative cutting tool when cutting mp4. You need to set Preconversioncommercialremoval to false.
Also note that MCEBuddy can't put quotes around the extension, it can replace the <file_name_withhout_ext> with the necessary stuff and quotes, but can't go past it.
Instead why don't yo uuse the custom command I' included, there you can write a batch file to do the stuff easily and use the filename and add the extension yo uneed. Itll be more efficient and easier.