I created a proper Khmer opentype font with all necessary substitutions for the rendering of a Khmer syllable. When I compose the opentype features in Glyphs, an test them in the built-in preview, it manages well to combine and display them correctly.
Anyway, when I export the font to test it in InDesign, the distances between some of the glyphs are being distorted especially glyphs that slightly overlap to the previous one, they overlap intensively. I tried to disable automatic kerning, adjust the tracking in InDesign, yet it doesn’t solve the issue.
I just ran into the same issue. My old FontLab -> FDK workflow for Khmer requires that spacing marks and subscripts be defined as SIMPLE, or in this case “Letter” instead of “Mark”. For example uni17D21799 is set in the GlyphData.xml as Mark, but it needs to be a normal Letter with sidebearings. If I don’t change anything Glyphs strips the width and exports it as a Mark with zero width even though inside of Glyphs it has width and previews correctly. Technically it could be considered a mark, but it acts like a regular base glyph in terms of spacing. I just went through my Glyphs file and changed all the relevant glyphs from Mark to Letter (Edit > Info for Selection ⌥⌘I) and re-exported and now it all displays correctly in InDesign.