Lapped cars were spread throughout the top runners on the restart with two laps remaining, all but ending any hope of a grandstand finish.
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Third place finisher Winterbottom was even further back, tucked up behind Rick Kelly's Nissan.
While cars two or more laps down must drive through the pitlane before any such restart, there are currently no rules requiring those a single lap down to retreat until after the resumption of racing.
Winterbottom was further frustrated in the final two laps by a lack of blue flags, which are only shown after an instruction from race control.
“I think from a TV point of view it looks pretty average,” said Winterbottom of the restart taking place with lapped cars in the mix.
“They (the lapped cars) are all fighting each other and there were no blue flags being waved either.
“Normally you'd pull over (if you were a lap down on a restart early in the race), but they're racing for 15th or 23rd or whatever it was, so it's a tough one.
“Different parts of the race are deemed different things, but if that was the end of Bathurst it'd be an anti-climax.
“You'd have to see how they could do it, but maybe late in the race… with two laps to go they're not going to catch the train (if they pass the leader), so something could have been done about it.
“Big races shouldn't finish like that.”
Race winner Whincup admitted to being frustrated by a lack of blue flags earlier in the race, but was cautious on any call to change restart rules.
The six-time champion had already seen a six second lead evaporate thanks to the late Safety Car.
“I'll sit on the fence on that one, I'm not sure what's best,” he said of the debate.
“The thing is that you've got to give cars the opportunity to get their lap back (by passing the leader).
“You've got to be careful not to write their race off.”
Van Gisbergen meanwhile shrugged off any suggestion that he'd have been able to overtake Whincup for the win if he had not had to clear Pither and Blanchard.
The Kiwi was catching Whincup prior to the yellows, but had earlier been engaged in an extended scrap with Chaz Mostert.
“I think Jamie had a bit of extra grip, I'd used my tyres up fighting Chaz,” he said.
“The lapped cars are fighting for 83rd but they're still having their fight. It's a difficult one.”