Most fonts that include Greek glyphs simply contain them and contain, if they support polythonic Greek, all glyphs with diacritics as well. So, for example, a capital letter eta with the signed iota remains such.
In some fonts, however, things are different. For example, in the Garamond Premiere the approach is totally different. The uppercase eta with signed iota is present in its slot (uni1FCC) as uppercase eta + lowercase iota. Then, there is a system that involves other glyphs (always using the same example, the capital age with the authentic signed iota) and a rather complex mechanism of substitutions.
Now, what is the advantage of this second type of approach, which is also absent in most fonts from Adobe itself?