Well said, but at least they were not lying to you; just stretching the truth for the customs
Over-simplified is a great way to put it. My personal feeling is that they were looking for a way to limit the number of undeclared batteries, so saying "installed" automatically obliges to fill in all the forms for any spares in the box. It still hurts business like crazy, though. In the end, for your purposes, it might be cheaper and simpler to send more packages.
Perhaps you will feel the need to invent some really cheap flashlight (as in a plastic tube with 1 wire and direct-drive 5mm LED) that can take a few li-ions of various sizes and would serve as a product to install the batteries in.
I have a few dents on my skull and all the Doc's said it's no biggie. And they're not new by a long shot... had them for longer than I can remember breathing and still no issues.