Just to try and help explain why people think you have a negative tone: written words tend to be interpreted negatively by default since you can't hear the person's tone of voice, so you have to use extra words to reinforce your positive intentions, and avoid using phrases that can be construed as positive with the right tone but have negative connotations by default.

For example, "Why do X when you could do Y" assumes they were aware of Y and consciously chose X over Y. It is overly presumptuous especially since you don't know them. It also carries the implication that you think Y is a better "default" choice and comes across as a prompt for them to defend why they chose X instead. It might be better phrased as "Had you considered Y instead of X, and if so, I am curious why you chose X instead?"

Also the phrase "Why would you do X" kind of comes across as "Who in their right mind would do X". A better way to say it is something like "Curious about the use of X? In my experience Y works better, have you had a chance to try that yet?"