What appeared to be the problem is that I increased the allowed number of jobs from default 1 to 16, but only 10 users for jobs were created during installation. On this rare occurrence that more than 10 jobs could be created, Guix was not able to do so and crashed.
I was able to continue by setting max-jobs to the number of users or lower. Suggestion: have Guix ensure not try to use more users than available. (Why does it even need a user per job in the first place?)