The character in question is Ἄ
U+1F0C GREEK CAPITAL LETTER ALPHA WITH PSILI AND OXIA and we find, in lgrenc.dfu
,
\DeclareUnicodeCharacter{1F0C}{\ensuregreek{\accpsilioxia\textAlpha}} % Ἄ
and in lgrenc.def
we see
\DeclareTextCompositeCommand{\accpsilioxia}{LGR}{\textAlpha}{>'A}
Thus the character translates directly in the combination >'A
. In the Greek fonts, >'
is a ligature and some fonts may provide a kerning between this character and the letter A (which is used to transliterate the Greek Alpha). For instance, if I remove the call to ebgaramond
, the tracing by TeX shows
....\LGR/cmr/m/n/10 ^ (ligature >')
....\kern-0.83313
....\LGR/cmr/m/n/10 A
But when ebgaramond
is used the same combination produces
....\LGR/EBGaramond-OsF/regular/n/10 ^ (ligature >')
....\LGR/EBGaramond-OsF/regular/n/10 A
No kerning. Can we add it in this case? Yes, we can.
\documentclass{article}
\usepackage{ebgaramond}
\usepackage[greek]{babel}
\DeclareTextCompositeCommand{\accpsilioxia}{LGR}{\textAlpha}{>'\kern-0.15em A}
\begin{document}
\textgreek{Ἄνθρωπε, οὐκ οἶδα ὃ λέγεις.}
\end{document}

You'll need to fix other composite commands, I believe, but the idea is the same.