In Glyphs 3, when a glyph contains only components and is not automatically aligned, automatic alignment is still applied on export. Here I make a /dieresiscomb from two /dotaccentcomb.
(Disabling automatic alignment globally in the font info works, but I use automatic alignment all over my project and do not want to disable it globally.)
If I disable auto alignment in twodotshorizontalbelow-ar and place the dots side by side, everything looks fine.
But if I open the edit window for the yeh-ar glyph, auto alignment switches back on. It also switches on in each related component glyph i click on in font view.