Yes, if there is a project folder, it generates a file in the project folder for you. The only way to make a project use a project folder later is by editing the XML: add the line <property name="shotcut:projectFolder">1</property>
AFTER the last line containing <tractor (assuming you use the timeline in your project).
The property was already there. I changed the value from 0 to 1 and it now records a voiceover#.opus file in the same folder as the mlt file without a file name/location prompt.
Not necessary but am curious…
Is it possible to set a subfolder for these recordings? e.g. Audio
No, but you are encouraged to copy or move any media that you manually add to project into this folder, and then it makes a lot of sense to use sub-folders. We just have not yet added these layers of complexity into the app.