I'm speculating, but I suspect that anyone using Co-dfns output will be running it on a private bank of GPUs over a large private data-set, so I suppose the AGPL won't ever matter for them, in practice.
You are right, however, that you can use the free, non-commercial Dyalog to run the AGPL Co-dfns. Co-dfns is both a commercial and a research enterprise, and so it is important to me that the ideas in the compiler are manifest openly to the public, hence the open-source nature of the project. However, it also needs to fund that research somehow (have you ever tried to get a grant to write APL? Hahahaha!), and so commercial uses need to be managed in a reasonable way, namely, something mutually equitable.
Some interested parties are working to use Co-dfns in public facing services, and not just private data sets. One group is very slow moving, but we're exploring the possibility of a rewrite of the cryptographic stack.
The Co-dfns work is run like an Open Company however. You are welcome to submit contributions (see the README for more information) as pull requests and can onboard yourself at your leisure. I'm working to encourage more people to support the funding of Open Work on Co-dfns, but that's a long, slow process.
So, yes, generally speaking the compiler is designed to be used in conjunction with the host of additional tool support you get from Dyalog APL (the interpreter). However, Dyalog makes it as easy as possible to get a copy of the interpreter.