Can rally compare how different index/cluster mapping/configurations perform?
yes, you can do this with Rally. See the docs on options how to run benchmarks against remote clusters. If you want to compare different index settings or different mappings, you'd most likely need to write your own track because otherwise you don't have any control over index level settings / mappings.
You should setup a dedicated Elasticsearch metrics store because you then have access to each individual metrics record that Rally captures. To get started you can then use Rally's tournament mode but for more deeper analysis you should famliarize yourself with raw metrics records and do your analyses directly in Kibana.
Regarding benchmarking methodology, you should run several iterations of your benchmarks before you draw conclusions because you need to also consider run-to-run variation.
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