I did a little experiment: I removed adwaita-icon-theme.tcz and hicolor-icon-theme.tcz from all .dep files in my optional/ directory.
Then I removed adwaita-icon-theme.tcz and hicolor-icon-theme.tcz themselves from optional/ and rebooted.
Now I'm in a running system without any trace of those two icon themes. Filezilla looks exactly the same including the faint checkmarks.
Gnumeric is missing some icons (has a little terminal screen instead of the expected graphic), but checkmarks are the same faint ones as before.
Conclusions:
In the case of filezilla, icons are built-in to the application and checkmark is handled by gtk3 directly.
In the case of gnumeric, icon theme's icons are being used but the checkmark is handled by gtk3 directly.
I don't know if gtk3 handling the checkmarks directly is due to a bug (where it can't use Adwaita's dark check mark) or intentional. I think if it were intentional, they would have gotten the colors correct.
I know sometimes gtk needs "theme engines" (e.g., murrine) in order to fully use a theme. Maybe gtk3 now needs one of those engines in order to use Adwaita's icons AND ui .svg files?