Hi, Bob, the Adobe Glyph List is deprecated. It has not been maintained, as it was an unfortunate idea to begin with. We largely ignore it (except for some of the names which were good ideas individually).
The PDF text-copying issue is known to us. It is indeed a problem, but no efforts on the font side will fix it. The attempt to re-construct text from named glyph fragments was an idea--unfortunately, an idea that could never work in general. It rests on severe assumptions about how glyphs might be assembled to form other glyphs, which would be an unworkable restriction for many font designers, and which are not followed in practice. For one example: a ligature glyph might be formed by several different combinations of characters. Therefore the mapping from ligature to text cannot generally work, as it's a one-to-many mapping. But it gets worse than that. Because of this, for complex text including combining forms and ligatures, copying text from PDF often fails, regardless of the font used. It's especially catastrophic with Indic text, and often can't reconstruct anything readable. The solution for PDF is to embed the Unicode text. You talked about other practical considerations regarding unencoded glyphs. First, the font's lookup tables (including the ones you mentioned) may indeed refer to un-encoded glyphs (a main purpose of the Private Use areas in Unicode is to provide slots for such glyphs within a font). The purpose of these is to go in the opposite direction from the text-copy issue--from encoded text to graphical rendering. It is to be regarded as a reference to a glyph *internal to the font*. These references are used by the font rendering libraries, but should not normally be accessed from application software. The mechanism works so long as the glyph names are unique, and so the AGL has no bearing on the subject. Second, special-purpose applications can refer to unencoded glyphs in special-purpose fonts in multiple ways, including glyph number and glyph name. By definition, there is no standard for this, so it has nothing to do with Unicode, and by the same token has nothing to do with the AGL. FreeFont is explicitly and essentially a Unicode font. We would consider re-naming a glyph in the interest of clarity or internal consistency, but *not* to refer to unencoded glyphs from application software. Cheers!