The author might have a different experience, but for me it's mainly anything that a) depends too heavily on a plethora of GNU tools and b) anything that's about deployment and installation. You're basically running on a different Unix system, so if you deploy to a Linux server, you'll probably encounter quite a lot of differences - mostly deployment, but also libraries, syscalls etc. Quite reminiscent of the days of different commercial Unices, where the compatibility of e.g. AIX and HP-UX wasn't exactly 100% (I'm sorry if that caused some violent flashbacks for veteran developers)

Also, OS X is usually behind even compared to Linux distros with fixed releases (i.e. not rolling). You get your basic Unix software in one fell swoop, with the occasional update through a dot version. Apple doesn't provide a pkgsrc or even a rpm/deb packaging system. There are third party efforts, like MacPorts, Fink or – as the author mentioned – Homebrew, which is more similar to BSD's package tree or Arch's AUR (basically a git repo of Ruby build scripts).

Nevertheless, these add on to your system, so aren't really integrated perfectly. Also, compared to Debian or Arch, you'll have a smaller package list (esp. true for Homebrew). So it might just be easier to install some stuff from within a headless Linux VM.

Heck, I've been doing something similar even when I was running Linux as a dev environment. Your deployment environment might be quite different, and I like to do some local testing first – doubly so if your company doesn't even have a proper testing/integration environment. I had an Arch PC, but deployed to both somewhat recent Ubuntu machines and ancient SuSe installations. Now, I often work on OS X and deploy to a CentOS VPS. All good use cases for VMs – and the way described, where it's just a small headless instance in the background instead of a useless GNOME desktop-within-a-desktop is a pretty good approach.