If you want to argue that the terms of 2.3.035 should apply, then you must conclude that the remedies of 2.3.035 should be applied.
Do you really believe that the sprint trains should have been made to stop until every rider affected by the incident is ready to continue and has caught up?
It can be argued that there was a justice in what was done in terms of dismissing the time gaps in the spirit of 2.6. 067, even though the terms of that were not met (personally, I think that the future application of the rule becomes jeopardised by each misapplication of it, so, with regret, would not have been in favour of the neutralisation here); I don't think it is tenable to try to apply 2.3.035 here (and I do not believe that it was cited in the decisions about, eg, Yates and the collapsing Col d'Aspin marker or Froome and the camera bike on Ventoux)