Q:

Git ignoring gitconfig? 

It appears Git is ignoring ~/.gitconfig
$ git config --global core.filemode false

$ git config -l
core.filemode=false
core.filemode=true

So now there are 2 entries for core.filemode and git is still not ignoring filemode changes
$ touch modetest

$ git add . 

$ git commit -m test1
[master (root-commit) 320cfe4] test1
 0 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 modetest

$ chmod +x modetest

$ git diff
diff --git a/modetest b/modetest
old mode 100644
new mode 100755

Based on torek’s answer, I added this line to my .bash_profile
[ -d .git ] && git config core.filemode false

A:

When creating or reinitializing a new repo, git init always sets a new value
for core.filemode based on the result of probing the file system.  You'll just
have to manually:
git config core.filemode false

Or:
git config --unset core.filemode

to make it respect the one in your ~/.gitconfig.  If you run git init again
the per-repo setting will go back to true on your system. 

A:

Maybe a bit overkill, but in Cygwin this bothered me enough to dig into the issue more.  When git is built from source code, it checks the file system it's built on to see if it understands executable bits. 
I went ahead and built git from source on my Cygwin system and installed it to a local directory, then added the binary to my path.  The basic steps are:
cd ~/
mkdir git
cd git
mkdir inst
git clone -c core.autocrlf=false https://github.com/git/git.git
cd git
NO_TRUSTABLE_FILEMODE=1 make prefix=/home/[username]/git/inst/
NO_TRUSTABLE_FILEMODE=1 make prefix=/home/[username]/git/inst/ install

Then add something like this to .bashrc:
export PATH=/home/[username]/git/inst/bin:$PATH

Of course, that build won't work unless you have all the build dependencies installed in Cygwin.  With a little poking around I was able to do it without too much trouble.  Now git init and git clone on that system defaults filemode to false.  The trick is defining NO_TRUSTABLE_FILEMODE for the build.