Hello,
I sent a file to JLCpcb for manufacturing and received this in return.
" … we’d like to confirm an issue found by the engineer during the generation of the production file.
As shown below, the circles in the outline layer and the holes in drill layer are in the same place. Shall we proceed as per circles in outline layer or as per holes in drill layer? "
" It means keep out region as shown in the picture "

And to be honest, I don’t really understand the concern. I don’t see any difference in the size of the holes in the property of the prints.
A little help from you would be greatly appreciated.
(Sorry for my poor English, my native language is French.)