The first point I interpret as "colourful arguments are avoidable and bad", with which I agree.
The second point I interpret as "colourful returns are unavoidable but good", with which I disagree - even if that interpretation is too strong and is more "... are unavoidable".
A function's type is its full signature, including inputs and outputs. When you have first-class functions, you have values with function types, and those values are inputs to other functions. Necessarily, then, if you colour outputs you have also applied colour to inputs.
Transposing a vector of things to a thing of vectors is an example of where colourful output forces colourful input. If you cannot abstract over abstractions, you must write and re-write the sequence function for each abstraction.
I'm in agreement with your closing paragraph's sentiment. That HKTs aren't a broadly adopted solution is something I accept, but I reserve the right to low-key begrudge it.
(And the more I write about this, the more I wish the original article had used "flavour" rather than "colour" as I try and probably fail to find phrasing that doesn't simply sound like portions of a racist rant.)