Git rm -- Git add-A after cached changes permission of the file

I'm going to send you a file.

 git rm -- cached text.php

After removing it from the stage as ,

git add-A

as

git diff 

If so,

old mode 100644
new mode 100755

he said.Go through a lot of things

 [core]
filemode=false

I understand that if you add to config, the permission changes will be ignored, but I don't know the fundamental reason, so I would like you to tell me about the following two things.

なぜWhy do you delete it from the stage → If you upload it to the stage again, the permission will change
②If you look at the file itself in ls-l even though the permission has changed to 644→755, you can see that the permission is -rw-r--r--, not 755
③With git diff

old mode 100644
 new mode 100755

I want to delete what says

Thank you for your cooperation.

[Environment]
Guest machine: Run centOS 6.6 in vagrant.
host machines:macOS
In , the contents of the vagrant are fiddled with phpstorm from macOS (without vagrant ssh).