Per my knowledge, there is no option to automatedly set what folders are visible or not in this OneDrive dialog box. The OneDrive dialog box shows all folders by default.
Meanwhile, to get this option in the OneDrive, I recommend you give suggestion in the feedback portal and help to make improvements. Many features of current products are designed and upgraded based on customers’ feedback. With requirements like this increase, the problem may well be released in the future. Thanks for your understanding and support.
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