I don't know if there's a better place to talk about this - if so, let me know where would be better and apologies for mentioning it here.
I'm using Gentium Plus and found a bug trying to typeset the word "praȷ̃nā" (wisdom). Here's a test string "aj a/jdotless (U+ 0237) a/jdotless/tildecomb (U+0303)" shaped correctly by HarfBuzz's hb-shape:

and here it is in CoreText:

Adding the combining tilde messes up the spacing.
So, is there a bad assumption in the font that just happens to work with Harfbuzz, or is there a bug in CoreText? (I am not using the Graphite shaper in Harfbuzz, so there's no Graphite magic happening.)
Comments
I get similar spacing problems to those you illustrate with Apple's own fonts, e.g. Hoefler Text.
I have also confirmed that the problem occurs with other combining marks, not just U+0303.
I have also confirmed that the problem occurs regardless of whether the base letter carrying the mark is encoded as j or dotless j.
However, the problem does not seem to occur when any other base letter is used.
Will activate the Ned signal.