I don't know why the default is where it is, but the master is switchable on the C-30 and, IMHO, the master isn't great on that amp - to me it sounds best with it defeated (or on 10) with the channel volume cranked to the desirable level of gain.
And on the EF86 channel - my favourite - 'power amp interaction' is the essence of the amp's architecture (assuming you count the phase inverter as part of the power amp ...). It has a single gain stage in the preamp, and driving the PI and output section is how it gets its breakup - there is none in the preamp alone, as it has only one gain stage. If you have the channel gain high and the master low, you are hearing the phase inverter overdriving and the output tubes running (relatively) clean. If you have the channel gain lower and the master high, you are getting less phase inverter breakup, and as you increase the channel gain you start to overdrive both the phase inverter and the output tubes (and potentially output transformer and speakers). And on a C-30 it gets quite loud before it's breaking up, even in half power mode.
But in the Fractal world we are spoiled because we can set the scene levels anywhere so we don't need to crank the amp to insane volume levels to get breakup and we can set the master wherever it gives us the desired tone, regardless of how 'loud' we want the end result, and the preamp boost feature of the amp block allows us to drive the preamp in an organic way that - IMO - you just can't get with pedals (real or modelled). So - as with all amp models - I recommend you adjust the various settings, including the master and the preamp boost (if you're wanting to run it quite dirty) to get the desired tone each time, and don't worry too much about either the real amp or the defaults or expect that there is any particular rationale for the default settings.