Yes the small seed lot permit is a lot more useful than most people interpret it. Another confusion was that you could bring maximum 50 seeds of each type of fruit. The real meaning is that you should have 50 maximum in each bag. For example if you want to bring 500 mangosteen seeds you can do it. You just need to have 10 bags of 50 mangosteen seeds in each bag. The purpose of this rule is not to limit the amount but to make it very easy for the inspectors to visually inspect the bags through the bag without having to open each bag out and dump them out onto a table.
Just like the weight limit... I always read it that way and assumed 50 seeds max per species. Its a lot more useful being 1 species per bag with 50 seeds or 10 grams per bag (whichever is greater).
When I had the cert. I never mixed taxa in bags.
Also even if they allow some clean types of media... I figured it was easier on them (inspection-wise) if I packed the seeds with no media. You can have media on a trip- then wash it out just before heading home that way you make it easier for them (and if they are in a bad mood and likely to quibble about your media, better for you)
If you eat the fruits right before boarding your plane, then what you say is possible. And in fact having no medium inhibits the seeds from germinating. Which is also good because germinated seeds are no longer allowed using small seed lot permit. For germinated seeds now they require a phyto.
But if you eat the fruits let's say one week before you board the plane, hen it would be better to have them in medium. Many types of tropical fruit seeds if they dry out are kaput. So it is a fine line decision between having the seeds still viable and not having them germinate on you.
If you are going to hold seeds for two weeks before boarding it might be best to either hold them inside the fruit, or holding them dry for a few days and them putting them in a moist medium.
There is really no problem with having them inside medium for entering USA if it is vermilculite, sphagnum moss, peat moss, wood shavings, or moistned paper or cloth. It is more of a problem if you are entering Canada, NZ, or Australia. Those countries are a lot more picky then USA. Those 3 countries don't consider sphagnum moss or peat moss to be sterile medium, and so do not allow it.
The only medium you should totally avoid is moistened soil or moistened coconut. All coconut parts are prohibited into USA.