juliamono
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Non-var theta and epsilon
There have already been a couple of Greek issues, but there's two more small things I want to bring to attention.
The thing which I stumbled upon was that the θ (normal theta) character looks too much like a zero to me -- its width is pretty much the same, and the "horizontal" bar is slightly diagonal, which my brain parses as a diagonal stroke as in some typewriter fonts' zeros. This doesn't happen when the stroke is completely horizontal. Perhaps also the total width and the extent above the M-height play a role. Is that just me? And in certain resolutions, it is rendered as completely horizontal, which I find much clearer:

And then, when I investigated the whole alphabet, I got the impression that the blackness of the non-var epsilon is noticeably higher than that of the rest:

(Screenshots are from Emacs under Ubuntu.)
It might be you ... 😄 I think the theta is bit pointier at the top and bottom...?
I've tried to make all the thetas different:
You could try using the OpenType standard alternative slashed zero (https://docs.microsoft.com/en-us/typography/opentype/otspec140/features_uz#zero) if you often get the θ and 0 confused... Emacs should be able to handle that?
And there's an alternate 0 too, in StylisticSet 4, which will give you a zero without anything inside.
I can tweak the ϵ a bit some day...
Ah, with your resolution I see now that the bar is actually a wave, in which case the distinction is much more prominent. Then it's not even me, but my renderer + display :P
One more thing: at small sizes, the greek letters start getting a smaller, at least optically:

Is that also my system's (or Emacs') fault?
Once the glyph shapes are extracted from the file, everything about how they're displayed varies from OS to OS and application to application! It certainly looks like Emacs is opinionated when it comes to displaying Greek text, though - this is the way it looks normally:
Unfortunately I don't test on emacs (or most other text editors really - last time I tried emacs I had trouble exiting... 😄