This is a little bit confusing. For example my material is interlaced (and should stay that way) and therefore I do not need the yadif-Filter. So I was wondering if there was a way to directly create my own presets only using ffmpeg commands and without automatically added settings?
The UI sets some options to try make the result best match what the UI currently shows. The preset merely sets the UI, and the UI logic writes the <consumer> element.
When progressive=0 (as determined from the UI settings and not the preset you have shown), the deinterlace_method is not used. It is harmless to specify the method, and it is not a filter that is actively applied.
Shotcut is not a ffmpeg command line frontend except for the Reverse, Convert, and Extract options in the Properties menu. Rather, it is an app that uses the MLT API, which is a middleware that uses the FFmpeg library APIs among many otther APIs. If you want full control, you can save the job XML, edit it, and run it manually through melt (provided with Shotcut) at the command line. See MLT docs.
Thank you for answering so quickly! I also tried out saving the job XML, editing the element and running it with melt (melt job.xml) - that also worked fine and is a great option for full control.