The second image shows the selection option, which ever so often i click wrongly and delete my files from my computer entirely, i'm scared of that menu, a clear list or the like with a keyboard shortcut would settle my nerves much more, inside MusicBee i would never ever want to fully delete any files, always done in Windows Explorer, to keep better oversight, would love to see that menu entry gone, i would sleep better 
i am slightly confused by this. The default is always "Delete from library only" and all you need to do is click the "Yes" button or even just hit the "Enter" key.
I am happy to make the options wider apart and even add a Alt-Delete key action that only allows deleting from the library only
Hello Steven,
Indeed, I often hit delete and then quickly enter, without seeing the selection properly and then it happens, after a while i find my files are gone.
The issue here is that while the 2 options are needed and useful, once you have used the second option, delete from library & computer your files are send to Windows Garbage bin, in itself it's just fine and works as expected.
Now the next time when you use delete, the last selection is remembered and as pointed out, i'm not the only one falling for this trap, i have lost countless tracks due to this that it scares me.
I leave my PC on 24/7 as i can't sleep much and or long so i spend my entire life literally using MusicBee so the last selection is always on, if you off & then on MusicBee, it's per design back to default, that is correct.
I assume that this option remember last selection is there by design and that users have requested for that since long, no issue with that, if you could make a keyboard shortcut to the DELETE from library and leave the rest of the menu as is it would be fine, as simple as that.
To delete accidentally from library is never an issue as when you monitor folders it will be added fast enough again to your collection, when send to Windows Garbage bin and if you multi task much like i do, its over written in no time after deletion, that's scary...
Anyway, it's reassuring that you have joined the conversation, hopefully there is a simple solution, i will take the back seat now, as my worries have been noted, looking forward to an elegant solution, on behave of fellow users with the same worries I thank you for spending you thoughts on this...
Tony D, a happy MusicBee user

I have setup a long time ago ALT+C for conversion (send to file converter), it's setup-up to convert to FLAC, replace source, never had an issue, it's second nature now don't need to think or look
The next step would be ALT+X to DELETE (clear) SELECTED files... one can only hope...