I'll do my best, have a little too much on my plate at the moment to do immediate work on the guide, but I have been experimenting with mud/dirt & adding dents/rust.
The above is with the first coat of 'mud' and 'dirt' using a texture that Dr. Noooo created and put into the 'Tank Skins !' thread. I intend to add lighter coats for a fuller spectrum of dust/mud.
As far as your questions go;
The basecoat is essentially for uniformity and finding which pieces need to be painted. I do it as I've written in the guide - find the obvious parts, paint them, then start painting and checking in-game to see what I've missed and what I should not have painted. Those are the advantages of a basecoat. It also makes it easier later on when applying camouflage to make sure there isn't any overlap of edges if the camouflage paint is applied over a uniform base. Means you can also have the tank ready to be painted in a colour that you can experiment different colour schemes, rather than painting an entire tank in camouflage, not liking it and having to start from scratch.
Light/Dark & Dark/Light; It does affect it, quite majorly at times. When I repainted my Hotchkiss H38 premium tank I had the base coat in a brighter than was necessary colour, and when I tried to apply the green camouflage in my usual way, with Overlay mode, the paint came out a deep, rich yellow-brown. To counter this I used that as a 'basecoat' for the camouflage and painted the correct colour over the top with the mode set to Softlight and the opacity to 50%. It is something I will try to address with part 3, using both overlays and other methods.
Next, decals & blending/opacities; This was something that I was going to cover in part 4. With decals I find using the Normal Mode is fine, it just pays to play with the Opacity & Fill levels. These will adjust not only how opaque the item is, but how 'full' the colours look - lower fill should = more worn appearance. 'least thats how its worked so far for me.
Important thing to remember is that this is not a Masterclass in skin painting, I'm not 'good' enough or knowledgable in making skins to write something along those lines, this was essentially meant to be techniques I use to do my skins and may help other people to do theirs - a 'correct' and 'definitive' way to skin tanks this is most certainly not.
With the above said, I would really appreciate it if other skinners were able to give us an insight into their techniques, and if they wanted them put into the guide then I will with full credit.