The documents that came with my car include the filled-out PDI checklist. Section 4, "Under Vehicle," calls for the inspector to raise the vehicle on lift to full height and, among other things, install the body plugs. That item is checked off on my checklist, and indeed the plugs are installed.
I'm amazed to hear that some of your cars don't have the plugs installed. This is a very common item; Honda and other manufacturers have used them for years. You'd think it would be completely routine to install them. On the other hand, even if your dealer didn't really perform the PDI, I'll bet they were paid to do it by Honda. I wonder if any of you have the PDI checklist in your documents and it is not filled out or signed.
I work at one of the ports here in California driving new cars from ships that have arrived from Asia to the railyard where they will continue on their journey. Those plugs are in a bag in the glove box of most of the cars I drive, along with the key fobs.