While I think it has been covered a bit here, I think the amp does function as more than just a vessel for sound put in to it. Anything that is between you and the sound that comes out of the speaker is going to affect the sound, it's a matter of in what form will it affect that sound?

I remamber back in the 80's the local store I went had a guy that simply knew everyone big in the business and the collectable guitars that store got was pretty shocking. The guy wasn't a talker and had credibility in the biz. Point being, he had himself a Jose Aredondo modified Marshall head (originally a purple Plexi, I think). Short of it is, you see the the actually mods, you would think nothing of them. I recall the stuff being really messy to look at but the sound of the amp was massive and I mean MASSIVE. The local guitar tech was good at some pretty spiffy amp mods himself and look at it and thought that the mods weren't revolutionary but the configuration and even some of the lack of 'clean' wiring contributed to the tone. I was told that Jose didn't really much care about tucking wires or anything, just attach point 'A' to point 'B'.

So, I think any resistance in the chain will affect the sound and sometimes fro the better and sometimes...not so much. Not all circuits, wire (gauge) and all that are made equal so it all is bound to affect the sound.

The extent to which each element affects tone from the type of pots to tubes all gets in there.

While the best tone I ever had was on an amp that should not have had great tone, it was because it had a great clean channel and the effects I put in front of it sounded great through that amp. I tried the same set up with another amp and it didn't translate.