There’s no need to do this in two commits, you can add the file and mark it executable in a single commit:
C:\Temp\TestRepo>touch foo.sh
C:\Temp\TestRepo>git add foo.sh
C:\Temp\TestRepo>git ls-files --stage
100644 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 0 foo.sh
As you note, after adding, the mode is 0644 (ie, not executable). However, we can mark it as executable before committing:
C:\Temp\TestRepo>git update-index --chmod=+x foo.sh
C:\Temp\TestRepo>git ls-files --stage
100755 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 0 foo.sh
And now the file is mode 0755 (executable).
C:\Temp\TestRepo>git commit -m"Executable!"
[master (root-commit) 1f7a57a] Executable!
1 file changed, 0 insertions(+), 0 deletions(-)
create mode 100755 foo.sh
And now we have a single commit with a single executable file.