That doesn't affect anything other than the
default conversion output.
And conversion output profiles don't really have any meaningful effect except for setting the maximum supported image resolution on a device. If set to a lower resolution than the source images in an ebook, they will be downsized to save size.
As always, previously converted books have their settings saved, and the defaults only affect newly-converted books. Using Bulk Edit mode, you can clear previous conversion settings if needed.