choosing colours for internal carpentry, windows and and floors

Its personal preference to a large extent. I personally do not like timber (varnished or otherwise) skirtings and architraves. I prefer to see them all white, or in a few specific cases a colour that serves a particular purpose. But on the whole, white. But that's just me. Its easier to avoid the 'lots of different wood types' if you paint the skirtings as you avoid having two expanses of different woods together. I'd be more likely to go with white architraves and timber doors, though at the moment all the internal doors in my house are painted, and I like them.

I had all new double glazing and would have liked a coloured pvc outside, but it was ridiculously expensive and I didn't like any of the standard colours that were normal price. The salesman persuaded me to have dark grey outside and white inside, and it has worked extremely well, I am delighted with it. The house outside is white so the contrast with the grey is nice. I would not want black or dark grey inside I think it would make your room options limited and white looks brighter.

Within limits I think you can mix tones and timbers in a room just avoid things that shout at each other. For example a yellow pine floor and dark polished mahogany shelves would not do anything for either of them. On the other hand some light floors and dark wood shelves could work quite nicely, there isn't an actual rule, it depends what kind of look you prefer.

The most jarring effects are when you randomly mix, say, rustic and modern, or are so anxious not to make a 'mistake' that you end up with something completely bland and boring. But an interesting piece of antique furniture, or an item that is pleasing but of a different era can be added to a modern room and look very appealing. I personally prefer eclectic to matching sets, but even if surfaces don't match, they should complement each other. I think this is easier with at least some painted surfaces.

My only advice I could give is don't have the interior of your windows black.
It will limit what colours you can paint walls in the future.
I love timber especially oak, we used in our new build,the trick we used by from carpenter is use oak with different grains rather than different shades.
It was used to great effect on our kitchen stairs ect.
We also used the same tip for choosing wood effect tiles.
Keep the tone of the colour the same and use the grain to give different effects.
Only thing to note it took longer to get the materials to suit,and slightly more expensive as more materials were needed to get the desired effect.