I think there is a lot of confusion about tracing settings and not enough clear documentation. This is an area I'm looking into at the moment.
So far, I've discovered that the powershell commands change settings in the MSCRM_CONFIG database and not the registry keys. In fact, my experience is that you can enable two sets of trace files, one with the powershell commands and one with registry keys.
They seem to work independently.
I suspect that the powershell commands cause tracing to occur on all CRM servers in a deployment whereas the registry keys only apply to the one server but I have yet to prove this.