I have a question about this pipeline. Is it suitable for pure genomes (not metagenomic bins)? If not, from a conceptually level what makes this pipeline suitable for only metagenomic MAGs and not single-organism genome assemblies?

Even if the intention of the pipeline was to use with community data, you can use any number of genomes from data from isolates to communities. @Thomas Mollica’s recent question was actually regarding an experiment with an isolate. I think this pipeline is the simplest nf-core way of just mapping to one or more prokaryotic genomes. Which type of genome -- classical isolate genomes or MAGs -- doesn't matter at all more than that the more complete and less contaminated the genomes are the better.

But it’s only good for genome mapping between prokaryotes? If I have a eukaryotic assembly and I want to do a whole genome mapping to another genome this pipeline isn’t the right tool for the job correct?

That's correct. It's essentially the exon-introns that hinders this application. What I think can be done is to map to eukaryotic transcriptomes, i.e. mature mRNAs.