What I'm wondering is whether two separate applications can be set up to communicate automatically, with one handling messaging and the other being responsible for encrypting and decrypting the data.
What would be against the law in that case? The messaging app? The encryption app? Or the interaction you are doing in that moment?
Of course these laws are dumb, but that doesn't mean they can't be (mis)used to get the desired effect.
Does Android facilitates IPC and services?
You can already install a mail client with PGP-support. Will K-9 Mail get in to trouble if a million users in the EU started privately exchanging keys and using GPG with K-9 Mail? Who knows. These laws are not about such practical details. This is about unlocking massive amounts of signal intelligence to do… who knows what, and those large communication platforms are juicy targets. All it needs is a law to coerce them to cooperate.
Don't expect reasonable arguments from the proponents of such laws, and don't expect to be able to avoid them for millions of users with clever tricks; you'll still fall foul of the spirit of the law, if not the letter.
Actually police and various agencies do, because when most people aren't encrypting, the few that do are suddenly interesting. Some of them will turn out to be organized crime, but some of them are just adults who want to communicate privately.
That might be the next step. Banning encryption. We live in a strange world right now.
What some law-and-order types (globally) want, is the means to scan, peek, or otherwise access private communication, especially if that communication is provided by a service used by millions. You can encrypt all you like, but if you use WhatsApp or Signal, laws like these force those services to create a way to eavesdrop. How is probably not defined in the law. Client-side scanning before encryption, having those services act as men-in-the-middle for each conversation; this is all fine, and can use encryption as usual. As long as certain agencies get to have a peek somewhere between those strongly encrypted tunnels.