Hey GU-11, sorry for the delay replying. The thinner is what the paint is made of before pigment - its the solvent. It's the main part of the paint in this case.
Stirring or shaking? No scientific difference I'd say other than I stir and shake my paints, no differnce. Stirring DOES help pick the solids off the bottom so it can make a difference if the paint has been sitting around awhile. Shaking does make air bubbles, but they of course go away.
About 1/3 of my Tamiya paints are mixed colors I make and keep for projects. No difference again. Many are a few years old too!
If you are brushing paints on by hand, layering can possibly take up older coats of paint. Brush GENTLY with thin top coats (like for effects). A thick coat WILL cut through to the lower coats since its "Wet" enough to act as a solvent still. I dry brush Tamiya paints with no problem. I have had wet top coats take up parts of the lower.
If you use water based on top of enamels, no problem. Enamels on acrylics are also usually alright. The different solvents are litterally liek trying to mix oil and water - litterally. I hope that helps! - MT