There are at least 3 kinds of boot behaviour with a USB3 drive. On older Macs with USB2 ports there is no problem booting because the drive connects in USB2 mode. For newer Macs such as yours, it is possible to boot in USB3 mode. And for those in the middle, like mine, it is necessary to force USB2 mode to be able to boot.
I got started on this exercise trying to boot from a USB3 drive set up as encrypted using Disk Utility, exactly as you did. I blamed the encryption, then discovered that an unencrypted USB3 drive was also invisible to the boot ROM.
Once I got the idea of connecting my drive via a USB2 hub, both encrypted and unencrypted USB3 drives showed up in the Option Restart screen, could be selected, and would boot. With an encrypted drive, a dialog popped up asking for the password, and then everything went normally.
It's clear that for my vintage of Mac the boot ROM was forgotten when USB3 support was being implemented. I suspect that a year later they tried to add USB3 to the ROM but only did half the job, forgetting the possibility that the drive might be encrypted.
If you have access to a USB2 hub, or to a USB2 cable that will plug into your encrypted USB3 drive, please try an option/restart in USB2 mode. I predict that the drive wll show up as bootable, and that you will be able to enter your password and boot from the drive.
It would be really disappointing if your newer boot ROM has lost the ability to boot from an encrypted drive, even in USB2 mode.
The fact that there are Macbook models in the field that do have USB3 support (even if it is incomplete) improves the odds that they would be able to add that support to my vintage of Mac without a lot of effort. Let's keep this topic hot in the discussion forums in the hope that fixed boot ROM images will be released for all USB3 Macs.
I have not had any response yet to my formal bug report filed with Apple. I'll let you know their reaction when it comes.