My claim is that anyone that uses Bitcoin as it is meant to be should absolutely not be concerned over fungibility.
I agree with that, as stated. Clearly if you read the whitepaper or satoshi's early writings it was not intended to pay attention or attach any significance to coin histories (which were viewed as an implementation detail), but people do, and you can't stop them.
I absolutely disagree with your conclusions, outputs are only non fungible in transactions involving third-parties which is not representative of Bitcoin's design.
This is incorrect. Any counterparty to a transaction can define things any way they like. If someone doesn't like your coins they can choose not to deal with you, or charge you more. It doesn't take a third party to impose such a view. It is purely a social convention how much weight to attach to to the history. If it becomes widespread, then it won't matter what third parties say, because people won't want coins with problematic histories. If history is widely ignored, then obviously it won't matter.
The important point is that nothing about the technology forces people to behave in one manner or the other.Moreover it can certainly be argued that these occurrences are marginal and nothing more than distractions.
I guess that depends whether you are the one dealing with the "complications" related to people paying attention to coin histories. I know several such people personally. It isn't marginal to them.