You're right that Ancestry.com is focused on mtDNA, but 23andMe actually uses a custom Illumina microarray with autosome, allosome, and mitochondrial targets. Here's a study where 23andMe used their (old version) chips to replicate a bunch of known genetic associations, most of which are autosomal: http://journals.plos.org/plosgenetics/article?id=10.1371/jou...