Struggling with the same issue. It seems like Glyphs is generating an .altVar01 character in the variable font file, choosing the bracket alternate as the default and not making the substituitons. The layer setup has been greatly improved though 
I have the same issue in Glyphs 3.
figured it out - https://glyphsapp.com/news/glyphs-3-make-things-you-love
There’s a rundown of the new Variable substitution export in this blog post, you have to create a the alternate glyph and define the substitution within your feature code, using ifdef VARIABLE (search for that term in the blog post).
It works as long as you remove the previous bracket tricks
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Thanks @rosaiani, that sounds interesting, but I was talking about something else. If I have understood @GeorgSeifert correctly, this feature code does not need to be written manually anymore; it should be automatically added to the GSUB (as well as the alternative glyph for switching) when the OTvar is exported. Already the later builds of Glyphs 2 were doing this for brace layers, but not for bracket layers.
Is it correct that Glyphs 3 should also be doing this for bracket layers and if so, when will it be implemented? Or is it already implemented and I am doing something wrong?
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It looks like it has changed from 2 to 3. I had it working in 2 and lost it on 3, hence the quest to understand what was going on. It really is easier to manage the Glyphs 3 way, but it takes some getting used to.
In Glyphs 2 it was only possible to have bracket layers and Glyphs exports the Feature variation. That is still possible and now it works better with multiple dimensions. We added the manual option to write the feature variation code yourself as setting up the bracket layers, specially if you have more than one break points is cumbersome.
Thanks @GeorgSeifert for the reply. But when I export the OTvar, there is no <FeatureVariations> section in the GSUB, even though all the bracket layers have been set up. What might be going wrong?
Can you send me the file?
Appears to be broken in OTVar exports currently. What does work is a condition in feature code though. Or a little patience until the Bracket layers are sorted out.
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no. thanks