So that's not confusing then...

As I read it, the rule is internally inconsistent (at least in intention, or the example is very misleading). It says the rule applies to a driver "
who has stopped after the stop line" (61(1)(a)) and provides an example consistent with rule 128 and that the driver can drive through, but only in circumstances that are not permitted by 61(2).
The language in the example implies that, for the purposes of this rule, the definition of intersection is anywhere beyond the stop line (which is inconsistent with the definition in the dictionary). The term
proceed through implies that entering the intersection has already occurred once the driver passes the stop line. Otherwise, that term could easily be replaced with
enter to give it a meaning consistent with the definition of intersection. That is;
(as it appears)
A driver may stop after the stop line at an intersection with traffic lights showing a green traffic light, and not
proceed through the intersection, because traffic is congested.
(as it would need to be if consistent with the definition of intersection)
A driver may stop after the stop line at an intersection with traffic lights showing a green traffic light, and not
enter the intersection, because traffic is congested.
As written, if a driver had cause to comply with 61(5) they would have to have committed an offence under rule 128. Is the sole purpose of rule 61 to mitigate the consequences of someone cocking up under rule 128?