I think there's also a lengthy quarantine process.
I might be wrong on the quarantine bit because of differences between the US and Europe.
I did hear stories about things going into the US from Japan having to be bare rooted in Japan first, and then staying in a quarantine USDA plant for 2 years, before being released. But I was under the impression that this is changed. Also because there are Japanese sellers that have a certificate and that say they can sell through EMS to the US. It may still be that on the USDA side, they decide to hold up and inspect your plants a bit more before they release them as safe. There could also be a difference here between a consumer and a few plants, or a business with a whole container, or EMS mail packages. They likely will prefer not releasing your mail package with your life bonsai, while it is dying vs them releasing something they are not supposed to release yet.
As for the USDA permit. It is not a permit to import said plant. It is just that you are registered with USDA as a plant importer. Apparently, it is not so hard to get one. But by itself, it doesn't help you get your specific plant from Japan. The phytosanitary certificate is the big thing. The Japanese grower must already have demonstrated that their plants are disease free, over a period of years. Which means they are regularly selling international already and went through the entire process years ago.
And then you need to pay a fair bit of money for there be an plant expert at the customs to inspect and waive through your plant. You pay for them to show up, I believe. And then you also pay a percentage of the value.
There may be another inspection by the US customs, with again the same cost involved. Plus possible import tax.
If you are a commercial bonsai importer in the west, you probably have a Japanese agent to deal with all the issues on the Japanese side. Like transport, paperwork, dealing with Japanese bonsai nursery/customs/MAFF/USDA, So you'd have to pay them too.
The exception for research is very interesting, though. In science, we basically just ship everything and put in 'scientific sample' so customs doesn't grow crazy over the sample containing actual people's brain slices, or living genetically modified organisms, etc. Also avoids import taxes.