In addition, removing support for addEventListener('webkitAnimation...' and removing the mapping to legacy types in EventTarget::fireEventListeners/legacy types would be necessary to really remove these prefixed events.

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I have some numbers from chromestatus about the usage:
https://www.chromestatus.com/metrics/feature/timeline/popularity/18

PrefixedTransitionEndEvent: ~3%
PrefixedAnimationEndEvent: ~2%
PrefixedAnimationStartEvent: ~0.2%
PrefixedAnimationIterationEvent: ~0.002%

I would say the first three still have decent usage while the last one could be removed. In the meantime, I will add uma to track the usage of:
onwebkitanimationend
onwebkitanimationiteration
onwebkitanimationstart
onwebkittransitionend

I think all 4 have somewhat high usage. 
PrefixedAnimationIterationEvent is on the boarder, you could try to add it to ukm or try something with http archive. 

For the first three, could you:

i. Confirm if they are supported by other browsers (probably not),
ii. do a scan through the HTTP archive as mentioned in https://www.chromium.org/blink/platform-predictability/compat-tools to see if we can find usage there

It may be that most usage is just mapping to the normal events anyway, in which case we could still proceed with deprecation/removal.