"Set as default"-settings
With some tasks in Blender I always change the default values every time and there doesn't seem to be a way to permanently change them. I do a lot of audio mixdown from VSE, as an example. I always use wav but the default is flac, so every time (ok, once each session) I have to start with changing the format. Adding a way to set the current value as default would help a lot. There are other areas where I always use non default values, like the import images as planes add-on where I usually change 7 values (I got help at blenderusers forum to change the script itself to use my preferred values, so perhaps a bad example...) or the Performance settings in the Compositor. And so on.
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Set the settings that you want in Blender, than do
File > Save Startup FileSome of these things (like preferred export format) can be saved as part of your startup.blend. It could, perhaps, be more clear that this is possible, but it is possible.