Found the hiding layout master...

To those SL users compulsively obsessed with a clean & tight Slide Master... 📢

Oh, yes... I tried everything, like flagging the layout with a screaming colour, checking all the "real" slides one by one, etc. None worked. Even the much-touted AI couldn't help. 

Finally, I found the deletable layout hiding behind a pseudo-slide--the 'Draw from Question Bank' "slide" (quite surprised that it actually uses the 'Blank' layout secretly). And with much glee, I pressed the Delete button... and sharing the joy with (the select group of OCD users in) the community 😁

Steps: 

1. Go to Story View. 
2. Select each "Draw from..." slide (without entering it). 
3. Look up & see the "Apply Layout" drop-down box on the ribbon. After Step 2, it would be active now. Click on it. 
4. From the drop-down, notice which "Draw..." slide is using the deletable layout that's been bothering you. 
5. Apply the new (Blank) layout to that Draw slide. Now, the previously locked, deletable layout is freed. 
6. Go to Slide Masters & now delete that offending layout. 

✌️