TFA doesn't actually refute this point. (not a lawyer) One of the differences between European and US monopoly law is that US law requires that consumers be harmed, while european law just requires a lack of competition.
Thus, in the Europe, a "benevolent monopoly", so to speak, would still be regulated, even if it provided optimal outcomes to consumers. This is not the case in the US.
In other words, people bundling the apps because they feel it enhances the product may still be illegal in Europe, if regulators feel that competition is stifled.
For TFA to be a refutation of this point, it would need to be the same ruling in the US.
There is a difference in terms of how you go about proving "abuse," but it's a difference of degree, not of kind; in the US, there is more weight placed on "effects" analysis where you see if you can prove something bad actually happened, while in the EU it is often sufficient to show that the actions are the kind that are likely to result in bad things. But this is a generalization and both kinds of proof are considered in both places.
Let me clarify: the us, due to precedent, not statute, requires evidence of harm to consumers. The eu only requires evidence of abuse of market share (which could be read as either harm to businesses or actions which might harm consumers).
In other words, if chrome were the objectively best browser, requiring it be bundled could be illegal in the eu and legal in the us.
This is I think very similar to what you say in your second paragraph, but flavored a bit differently.
In any case, it does mean the article isn't clear evidence of harm to consumers or that concerned would pick differently.
