Fontself scales the glyphs so the exported font as a EM-size of 1000. Okay, great. So, what does it use for scaling? Does it take the original difference from the Ascender-guide and Descender-guide? Or does it take the largest glyph sets that to 1EM?
Replying to myself, Stack-Overflow style. Th question was answered by @franz by mentioning the documentation: https://help.fontself.com/en/articles/2040682-size-units-and-scaling
In short: make sure the first character you add is a square at 70% size of 1 em.