Will osquery daemon process auto reload when osquery.conf changes at runtime by user?

I don't know if it will, but there is a 'refresh interval' setting that should cause it to pick up changes: https://osquery.readthedocs.io/en/latest/installation/cli-flags/#configuration-control-flags

bear in mind that configurations for some plugins don't reload with that flag such as kafka topics.

flags file loads once at startup, iirc config file loads dynamic based on refresh interval