We decided to put some money on the table with the hope that someone will step in and fix this bug. This will benefit not only Zend Studio users, but all Windows users in the Eclipse ecosystem who want to use the dark theme.
We created a $150 bug bounty on the FreedomSponsors crowd-funding platform. Follow this link to open the sponsored issue. Since this is a crowd-funding platform, anyone else who is ready to give some money for resolving this issue is welcome to do it, so the offer becomes more attractive.
UPDATE. The bug has been fixed within days and it will be delivered with the Mars M7 milestone. Thanks to Fabio Zadrozny for his great work. Kudos to Lars Vogel for adding $100 more to the bounty.