New: ShareX (Mar 27, 2023), Platform 24.1 (Feb 13, 2023)
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There's another way to have Windows show custom icons for folders without interfering with other operating systems: set the System attribute on the folder (only System; NOT Hidden). If you do this, the folder will still show up in Explorer with its custom icon, and should allow Linux and others to write to it, unlike currently...
that.
I would agree if Explorer didn't have the Option "Hide system folders" checked by default. 
Why can't Windows use standard regulations?
As long as the Hidden attribute is NOT set, folders with only the System attribute still show up in Explorer, regardless of the "Hide system files" option. 
I've tested it myself.
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