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.