If you are a beginner, there can be a lot of questions overwhelming you to the point of paralysis. That’s totally normal, because everyone’s that confused in the beginning. It just take time and patience and dedication to get over that initial hump of feeling lost and frustrated (of course, proper guidance helps a ton).
The example texture you first posted–it’s really quite simple and I’ll demystifying it for you a bit.
Basically, take base photo textures that are shot with flat lighting so you get just the texture and no forms.
Then you just paint in by hand some subtle lighting information for subtle forms that you want to be visible on the 3D model–forms that won’t be modeled due to poly count limitations. You can do this by simply pointing in the forms on a separate layer (highlights and shadows, on separate layers each, so it’s easy to change one without affecting the other).
Or, some people might also utilize the dodge/burn tools directly on the photo layer (or a copy of the photo layer, in case the artist changes his mind and want to erase back to the original photo in some areas later). But beware that dodge/burn are tricky because they don’t just change the value–the also change the hue and saturation too, so if you don’t want unpredictable behavior, don’t use it. A better method I use is to duplicate the photo layer and use the levels or curves tool and create one copy that’s lighter in in average value, and one that’s darker in average value. These lighter/darker copies don’t deviate in hue/saturation nearly as bad as dodge/burn, so you just place them under the original photo layer and erase the photo layer to expose the lighter or darker layers underneath to get your highlights and shadows.
All of this is done by hand with simple Photoshop brushes, since it’s just very basic digital painting technique. There’s no need for any other type of tools at all–any decent digital artist can do this. If you can’t do it yet, then it’s just a matter of practicing your painting techniques until you can.
BTW, I used to be a full-time game texture artist for a few years early in my CG career, so what I wrote above is based on my professional workflow.