Exactly. In other words, when people talk about their favourite key, it will NOT just be treated in terms of its purest sound phenomena. Factually, different keys do lead to different writing for instruments and different qualities of timbres, it justifies having 'favourite' keys. However, if this thread wasn't specifically about somebody's favourite key which will inevitably be influenced by these aspects, but instead was more about the natural phenomena of sound in its purest cerebral form, then my response would have been entirely different.
These aspects are simply unescapable given the circumstantial nature that will surround and influence peoples perspective on key.
To try and compartmentalize it so specifically while hypothetically removing external factors is utterly pointless in this thread, and should be discussed as a separate issue in another thread, which could then be allied with a thread like this in due course after productive discourse on the matter has passed.
EDIT. On the first point in your post: The way in which pitch is manipulated (and other aspects) in many instruments will be influenced in different ways by the key it is being written in. Keys will encourage tendencies that relate to very specific technical caveats for a multitude of instruments. Seeing as when many composers write in keys, they truly do write in the key in a strict way, then how chords are spread through different instruments may change, and the actual bottom and top frequencies of those chords would change and likely produce a timbre that is in the very least not identical. A really basic example would just be taking x piece and transposing the entire thing up a perfect 5th. The timbre will obviously change, but then obviously the writing would most likely be poor, so notes will have to be rearranged, resulting in a different configuration of the music altogether which would again have different sound qualities to the original.
This specific aspect though should also probably be discussed in a separate thread. The main point of talking about it briefly here is that it is nigh on impossible to not attach key to other elements that are processed holistically in deciding on an answer to such a question. In short then, with regard to the question asked in this thread, practice can't be separated from the theory (unless you could successfully radically alter the way this question is perceived and what it alludes to for the vast majority).