Hey Alexis! Thanks for your reply!
I'm afraid the issue is actually on the export side. Try this: export a color map and a height map in Raw format, so notice they don't match each other vertically. Then export it again in PNG format and you have a match.
Another sign the height map is being exported with the Y-axis flipped happens in Unity. When I load a Raw file directly, it shows upside down in Unity Editor. If I flip the Y-axis manually during the loading, it matches the viewport in Instant Terra. Again, this is not needed if I export a terrain in PNG format.
What do you think? If you need any further assistance, I'll be here!