There is a difference in scale. For the research 23andme wants to do, they need to identify variants that occur in a significant part of the population (~1% or so). They need to do this because any potential drug/treatment would have to be developed for a big enough patient pool. Large population level genome studies like 1000 genomes and NIH All of Us studies are all aimed at finding those ~1% variants.

But if you’re looking for what is going on in an individual, then yes… SNP chip data isn’t as informative as whole genome (or exome) sequencing.