Dougmc, FWIW I take a crack at your questions, but bear in mind these are observational answers, I'm not a 'techie'.
1) The circuitry of many pre-amps is not stable when first turned on. Because of this many pre-amps have an auto mute function which mutes the signal at the output until the pre-amp has stabilized. This is certainly true of most quality tube units. My DAC's and CDP's also have a short mute period as well. If your amp was powered up, and your pre amp doesn't have an auto or mute function, or the mute is inoperative, the output energy could cause damage to your amp if not protected (usually a problem with lower cost SS amps - higher cost amps typically incorportae protection circuits which shut down the amp if, for instance, DC is detected, and some also shut down the output section to protect your speakers from damage) and possibly your speakers.
2) Speaker thump is caused by a transient originating in either the source or the pre-amp at turn on, turn off, or both. Some times it can be caused by faulty switches, etc.
3) I'll take a pass on 'inactive', except to say that in my tube stuff it is accomplished by reducing voltage to the amplifying circuitry to a minimum, or eliminating it entirely. When you 'turn it on' all you are doing is restoring voltage to full value...the rest of the unit is warmed up and ready to go. Probably similar for SS stuff...I don't really know.
4) Don't know about the operation of your integrated, but if you simply pull the cord on a lot of tube stuff the auto mute function on the preamp will not be engaged, the amp will have sufficent stored power, and any electronic garbage from the sources or pre-amp normally experienced in shut down will be communicated to the amp and potentially to the speakers. Damage in that scenerio, though, is probably highly unlikely.
Your first question to Dragon - If the transients originate in the source using the VC will reduce or eliminate them from appearing at the pre-amp output
stage. However, if the problem is at the pre-amp's amplifing stage turning down the VC will have no effect as the VC usually preceeds the amplifing stage. There is nothing between the pre-amp amplifing stage and the amp input stage except for a mute circuit if you have one.
Regarding your musing in your secord paragraph...Amplifiers do just that, if they are not amplifing they should be dead quiet (or at least the residual noise floor should be minimal (usually this depends on the efficiency of your speakers). It is not uncommon for there to be a small 'pop' on turn on or off off a power amp. Not a big deal. I've never had an amp damage speakers from turning it on or off, but I've had a few pop's.
FWIW, you would probably get a lot better quality of answers if you were to start your own thread. As it is, no one who has not already participated in this thread is likely to sign on out of curiosity at this late date. In fact, some who already did participate may have assumed it had wound down (they had already contributed as much as they had to offer) and didn't review it again. I'm very prone to do this myself.
Hope that helps a bit...........