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Here's an option. There are companies in China which sell standard enclosures for USB plug-in devices. They'll even throw in a color of your choice and a sticker. You'd have to redesign your board to fit their case, but that may be a lot easier than dealing with encapsulation.[1]

[1] https://www.aliexpress.com/item/1-pcs-szomk-white-small-usb-...

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The problem is that the U2F specification requires users to approve authentication requests by pressing a button and none of the existing enclosures have a space for one. Entirely coincidentally, the company behind it (Yubico) already had a design with a button because their original second-factor proposal had no other way of knowing you want to authenticate. It's a little pointless on U2F but the spec requires it.

You could quickly drill a small hole in each case, in order to fit a tall button like this one:

https://www.sparkfun.com/products/8605

Also, there's some U2F devices that trigger the approval simply when they are plugged in.

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