Plenty of interoperable encryption systems, they'd just have to use and support one or more such as GPG, PGP, IPSec, etc.[1].

[1] https://en.wikipedia.org/wiki/Public-key_cryptography

It wont break it. You can send and receive the messages. To decrypt it, you will need the same app as the sender used. Basically how it works with email. If you pgp encrypt the message and the receiver only has smime at the moment, they wont be able to read your message.

This .eu thing is about platforms providing an api to connect and exchange data. It's not about what data etc can and cannot be used.