On type & fonts

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One of the questions for which I have not found a good answer yet is this:
 
Imagine that a typographer/designer inserts a glyph directly via a layout application's glyph palette. Also imagine that this glyph is an unencoded alternate variant – usually this is accessed by typing (which inserts an encoded character) plus applying an OT layout feature.
Now the type designer faces two options when creating OT layout features, based on either of these assumptions:
1 This glyph is considered as the typographer/designer's explicit choice and final word, and should not be changed by any layout features applied to the text. (E.g. when selecting a special alternate with swashes.)
2 The typographer/designer used the glyph palette as a mere keyboard extension, because he cannot access a specific character on his local keyboard. This however means that if he applies OT layout features to glyphs inserted via glyph palette, of course these glyphs should be changed. (E.g. when changing numeral style.)
Which way to go? Both ways are equally legitimate.


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