Maybe it’s just me, but from what I see it’s a case of Crate, due to their small size, have never been able to have time to run both sales and make the game so Humble Bundle took on the role of selling (they were the only option to buy from for quite a while) and while Crate have wanted to have an option for upgrades, Humble Bundle were unable to supply this ability until they decided to manually run each upgrade request individually.
For example when I first supported Crate with a Patron pack there was no option for anyone to upgrade. It took a few months before Humble offered the manual option. The problem is that now the game is available via Steam as well, Steam does not do any manually upgrades or anything like this, so the upgrades are still limited to people who have purchased from Humble Bundle and the first post does clearly say that it is only down to Humble Bundle doing this manual option that anyone can upgrade at all.
So it’s not really Crate excluding Steam buyers, if Steam was able to offer to the same upgrade options as Humble bundle do then I certain Crate would announce and offer this. If anything Steam not offering this is not helping Crate in sales, so I don’t feel Crate is to blame here, they are doing what they can.

