When some of you guys say "clean DI" do you mean through a dedicated box rather than through the back of a head/combo? Or do you just mean pre-eq? Why is important to have a "clean" sound through the DI?
Great thread, btw.
If you're recording both a DI and a miked amp, the presumption is that you want to have contrast between them and also retain the option to have the DI serve as a "safety" in addition to another sonic choice, meaning that you can reamp with it if the miked amp has noise issues that are intermittent or that you otherwise didn't notice during tracking.
If the DI has already gone through some tone shaping in a pre amp, it's probably also had its' impedance changed as well in a way that may not be as easy to account for considering that the channel might be then routed to a preamp (or, later, a reamp box) that expects a mic level signal or an instrument level signal specifically, and it's just not going to be as plain vanilla as you may want for the DI. It's not entirely "direct" anymore.
And a lot of amps that have a direct out just don't sound as good as a pro DI box. There are DI boxes that cost more than amps, and you can see the cost in the parts.