The whole toilet seat thing is as misunderstood. If the Air force needs a new toilet seat for one of it's jets, and that jet isn't in production anymore, and you can't just go to homedepot for aircraft parts, then you have to order a bespoke seat.

Now setting up the tooling for an injection molded plastic seat, only to produce a limited run, maybe in the dozens, $10,000 per seat is a reasonable price.

I'm sure the Pentagon buys toilet seats at the regular price. The interesting thing about Pentagon bathrooms is that it has double the number it needs because of segregation.