Since the astronauts were up there planting flags... I'd think it's less about the vessel in space and more about making it clear that the land visited isn't considered claimed as part of the US.
If the distinction is that the US watercraft are military and as such are not subject to customs, then making it clear that returning astronauts are not on a military mission sends a diplomatic signal.
US Service Personnel don't follow the civilian process for Customs, so making astronauts actually follow the civilian process reinforces the non-militarized feeling for space.