@Adam Bower Thanks for sharing the discussion link, Adam. It definitely answered most of my questions about this 'Cleanup VCL file' setting.
So, I did saw this error in all 3 projects where I decided to turn on the setting and had exact same issue on publishing a design. Of course, I didn't realized what's causing the error until I get to the 3rd project.
But since you already did your study and jot down the cons of this setting at the other discussion, I think I'll not mess with it for now. I'll wait till it's doing what it's supposed to be doing.