It makes absolutely no difference, it's all a relative perspective. Having your loudest element at unity means that none of the other faders will even approach unity. THat's how I mix as it gives me an instant relative peak level of all other mixer channels simply by glancing them. -3dB on a channel means that it's half the volume of my loudest element (nearly always my kickdrum), it's as simple as that. Nothing else approaches unity. Of course, this means that the master bus will clip unless I pull down the fader but that's absolutely no sweat and has no impact on my mixing workflow. Going back and forth wasting time adjusting all faders when one reaches unity or when the master clips is extremely inefficient and not grounded in reason.
I'm not quite sure where you see I'm coming from. I'm talking from an extreme POV. My point is that people who are not to sure about setting levels correctly before mixing will, more often than not, will try to make things as loud as possible by cranking the gain way to high on a channel, boosting the bass going mad with processing will result in a crushed mushy distorted dynamically dry mess, pre master fader. May not say it's clipping, but it'll sound bad. No point cranking down the master to compensate for a terrible mess.
This has nothing to do with faders. Plugins can clip a mixer channel, but the channel itself will not clip, i.e. you will not hear any clipping artefacts. Going to great amounts of effort to achieve something that can be achieved simply by pulling down the master fader is not a good use of time. Everyone has their own mixing style and that's absolutely fine, but propagating myths about master fader = bad is not helpful.
Yes, nothing digital can go over 0db. Which is the main reason why it sounds bad! Values that sum to a value greater than 0db get chopped off. Period. This murders waveforms and you can see it as flat tops & flat bottoms. Where as in analogue clipping it still retain a rounded shape. So you may not be peaking, but you can still hear "clipping" from a) audio being crushed too much by processing (such as hard limiting) or b) audio getting chopped off It's not pleasant, and my point is being aware of your levels and setting them correctly. I rarely let my channels go above -2db when mixing I never let them touch 0db, and the I leave about -3 / 4db headroom before mastering the track. But that's how I like to do things.