Has it ever happened to you that the Math symbols like mu, Pi and Sum get in conflict with Greek glyphs you included in your font? Same goes for Omega/Ohm (the latter is the unit for electrical resistance), Tcedilla/Tcommaaccent, random localized or versions of the same glyph and whatever I am missing.
Do not have the problem currently, but wish to be prepared if it does occur.
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In such cases, it is then possible for the PDF creation app to end up using the glyph encoding or glyph name to determine what underlying character is. At that point, the PDF will still look and print fine, but an attempt to copy/paste from the PDF might result in technically the wrong character being pasted (though it might look very similar, depending on the font). Or an attempt to search the PDF for a string containing that character might fail, due to the character being unexpectedly different.
I don’t think these scenarios for PDF creation are terribly common any more. I don't double-encode glyphs because of habit and workflows I learned long ago. I figure I might as well make a bit more bulletproof font, as it were. But I doubt many users would notice the difference.