Well, that is an assertion, which I find hard to believe.
If your source would shed some light on why they think that the water quality would be affected then that would be helpful to understand what they are afraid of.
I suspect that they are proffering this opinion (making it up) because they want to sell you another system. Their salt electrolyser will function to its parameters (albeit poor) regardless of the cover is on the pool or not. That is my assertion and some science to back it up.
Personally I would suggest that you treat the person who told you that with the utmost suspicion and avoid doing business with them in future.
Andrew
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