Well - I do prefer a varied sound in the snare drum, and I think that the snare is the *worst* place to use triggers, unless you can do it very subtly. The snare drum is the most apparent and frequently played drum on the kit in rock music, so it totally sticks out when every strike is homogenous.
That being said triggering the snare can help out in certain situations (blast beats!) - but it's not a crutch. There is a snare trigger recorded for the new motW album, but since we haven't mixed it yet I've no idea how much it will get used.
In addition, when we recorded Bath/LYBM I was playing on two kick drums as opposed to a double pedal. Jim (the engineer/producer) and I worked for awhile to get the two drums to sound alike, and just couldn't do it. So we triggered it. So anytime there is double bass stuff happening on those albums you are listening to a mix of natural drum sound and triggered sound. Probably the bass drum sound on the new one will involve triggering, too.
Adam (from Killswitch Engage) who also engineers at the studio triggers both kick and snare on pretty much every heavy record he does. He's really good at it and can make it subtle enough, by mixing it in with the mic'ed drum sound, that you don't even notice in the final product. It just sort of beefs up the original track.
I don't know which Opeth thing you mean in specific but if it's from Still Life on I'm surprised - I would have thought the producer or whoever would catch something like that...It could be that he (the drummer) is sometimes hitting rim shots (snare head and snare rim at the same time) and that's giving the "snappier" sound. That's pretty much how I hit my snare drum every time, at least in the heavy sections. By this point it doesn't feel natural just to strike the head.
And yes, we overdubbed a ride cymbal part on Stones (which I was originally against, but have now come to like) and the big floor tom roll at the end of Garden Song.