This sort of “thump” is very difficult to prevent. Overall the SONOS designs are excellent at minimizing these thumps. In some respects it is similar to your sudden awakening from a sleep. For a brief period you may not be aware of which end is up. Certainly, you should not attempt to hit the ground running. Likewise, an amplifier typically requires a little time to start up. The traditional approach to amplifier design is to use a relay to keep speakers disconnected while the amplifier fumbles through power up. Depending the amplifier’s power and design, these thumps can be quite large, possibly speaker threatening. You are probably familiar with legacy receivers where there is no sound for 8-10 seconds after power up, followed be a quiet mechanical click when the speakers are connected.
The relays are a mixed blessing because there is a slight impact on sound quality, and in a few years there is often a relay reliability issue followed by a trip to the service center. With very careful design these startup clicks can be avoided, eliminating the need for a relay, but this takes some extra design effort usually reserved for the very highest of high end designs. Part of this messy design process specifies components that age in very predictable ways, these are more expensive.
Anyway, in your case a component or two in your SUB are on the edge of the expected aging profile and, as a result, the click has become more audible. In almost all cases there has been a very quiet click, likely buried in the ambient room noise, that you never noticed. Typically, once you are sensitized to the click, it will never go away, possibly becoming more significant as your attention focuses on it, regardless of the actual physics.
From my seat I can’t determine if your click is atypical, indicative of a pending service issue, or not. I don’t approve of the agent’s response. Two possibilities are that your ambient room noise level has fallen or you sit closer to SUB.