Isn't that amount of locking a bit excessive? For sure lock down the main system, but what's wrong with allowing exec on drives connected to the VM? Chromebooks still don't have much storage, and the point of locking down USB devices is because many cannot be trusted. For me, it seems that a simple (relatively) way to establish "trust" is to, first wipe the drive, and then encrypt it with a key tied to the Google account. The main caveat to this, that I can see, is that the drive would no longer be usable outside of ChromeOS or a Linux distro, depending on how the encryption is implemented on the drive (because, you may use LUKs in order to provide a recovery key, per se).
I understand it was not your original goal, but ChromeOS is still one of the best Linux distros I have personally tried, mainly because the stability is, to me, unmatched. However, not being able to run executables on external storage is a hinderance to my personal workflow. That said, if your minds are made up, I'll find another way.