[BUG] Don't save Merge Control in Preset

[Selur]

But the setting for displaying them "Show Merge-controls" on the "Misc\UI" tab is still not saved.

That is correct, since it's not a 'Vapoursynth filter'-option, but an option of the 'Filtering'-model. (It's part of the 'All'-preset and will not be saved per filter.)
This will not change.
If you want that option to be enabled by default, save it in your defaults

Cu Selur.