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To me Humble Bundle support with GOG Galaxy 2.0 doesn't mean much when you can't launch the game's you've downloaded and installed via GOG Galaxy 2.0 if you can't link them under the "Humble Bundle" bookmark after connecting your account (though the bookmarking feature itself is limiting to me as well since you can't manage them manually). Sure you could link them as "Other" platform that way but it seems like you're adding clutter and duplicate entries of those games, especially for the same exact version that you just downloaded/installed onto your PC. And speaking of dealing with clutter, can there be something be done when installing games that have multiple versions between operating systems and perhaps cut them down to just the operating system you're running on (e.g. Windows) and leave out the other systems unless you're using GOG Galaxy 2.0 on said operating system.

Another actual problem I ran into while connecting my Humble Bundle account to GOG Galaxy 2.0 is that it seems to obtain completely wrong games; I have Sonic & All Stars Racing Transformed on my Humble Bundle account, but for some bizarre reason it gave me Sonic & Sega All Stars Racing, which is not on my Humble Bundle account or even Steam account at all.

I also have problems with even using the *.ini file for Humble library integration and it keeps resetting on me and does not work at all for me. Also, what happened to command line support on 2.0? The old Galaxy client had it but it's gone in 2.0, which is not good because some users like myself use command line arguments enable features within the games themselves if supported (e.g. skipping intro videos, changing rendering modes, loading config files).
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As this is a community plugin, you should really post your issues with it to the devs. I do not have the rep to point you straight to the Github project page for it, but if you Google "galaxy integration humblebundle" you'll find it as the first result. Click the "Issues" tab to let them know of the problems you're having.

I hope this helps!