Personally I find the ergonomic issue with using a mouse (and why I don't use one) is the "gripping" action required to operate it - i.e. the hand has to be curled up rather than stretched out/relaxed.
I haven't tried one, but I would personally not use a stylus (or something that has to be gripped like a pen) for the same reason - the hand has to grip it.
With a trackpad you are not really using the muscles in your hand, so you are not holding it in constant tension. Your hand isn't completely stretched out - but it is relaxed, you are using the muscles in your arm to move it.
It seems to me that the issue isn't really using the muscles as such, but the quiescent state of holding certain muscle(s) in constant tension, which is the issue for me with using a mouse.
As well as the fact you don't have to grip it to operate it, with a trackpad, you only touch it when you actually want to do something with it, whereas with a mouse (and I guess a stylus as well) the temptation is to continue holding it between successive uses.
I personally use an Apple trackpad. It's probably not quite as accurate/quick as using a mouse, but the ergonomic benefits far outweigh the disadvantages.
The main issue for me with a trackpad is that you often can't drag far enough. The mouse solves this by being able to pick it up and put it down again.
The Apple trackpad solves this with 3-finger drag, if you drag with 3 fingers, if you pick your fingers up and put them down again within about a second or two then it doesn't interpret it as the end of the drag, you can put them down again at the other corner and continue dragging, this is an essential feature in my opinion. (This definitely works on windows when remoted into from a mac, I think it would probably work if the trackpad was connected directly to windows as well. You could always try it and send it back if it didn't.)