You didn’t do anything wrong. In fact, you pointed out something that (at least) I was unaware of. If you use git to clone the repository, the file permissions will be set properly. Using unzip will reset permission of files based on your current umask. According to a quick read of the unzip man page on my CentOS 7 system, I don’t see a way to preserve permissions on the files themselves. In this case, making buildutils/pbs_mach_type executable was a simple way to address your issue. Thanks for posting to the forum!
One note of caution… I see you downloaded a snapshot of the master branch. This is the bleeding edge development code that has not been subjected to formal testing by our QA team. If you’re looking for something that has been more thoroughly tested, I suggest you download one of our formally released versions here: https://github.com/PBSPro/pbspro/releases
I have verified that permissions are preserved if you download and extract the .tar.gz file for the 18.1.2 release.