@chrisakavern - I don't think the wording is the issue, nor are people unaware of the fact that calibre copies your input files. In fact many people like myself rely on this, and delete the source files after they are safely contained within calibre, leaving just a single calibre directory to have to backup.
It is just too dangerous an option imo - the number of times I have done a conversion and realised that I needed to tweak something else (maybe adding smart quotes, changing encoding, justification, doing a split, change heuristics, or...). With such an option you propose enabled the user gets only one shot to get it right, and if they screw up then they have the inconvenience of finding another copy of the original somewhere to put it back into calibre and start again (that is *assuming* they have the original copied somewhere).
So users will "play it safe" by not enabling it - and if no-one but yourself feels brave enough to use it that hardly justifies adding one more option to the already intimidating number of conversion options
I find it trivial with the various right-click Remove options or direct deletion in the Edit Metadata dialog to remove only the formats I no longer want after I am done with conversions. Yes it is an extra step - but it is a step that errs on the side of caution, just like Kovid adding the ability to keep original formats recently for same format conversions.
That particular default conversion page in your screenshot is my pet hate of the conversion pages btw - I have never in my life changed anything on it and and instead always switch to Look & Feel where the actual useful conversion options begin. So if anything I would like an option to not display those options
. Thankfully it doesn't appear for bulk conversions, but it would be nice to avoid it for single conversions too...