This is not an issue or complaint, but has been a frequent recommendation that the players on my server have been asking for me to post to Pixelmon. At least 50 people use the custom Shader on my server, and all of them that do use it say they would like to see this fixed, seeing as you do promote the Shader in your pictures.
Other mods have this issue too, where custom GUI's become brighter when indoors because of their transparency, and all of the users of the Shader have said they would not mind if the sidebar became non-transparent, seeing as the Pokedex itself is taking up at least 3 times as much room on the other side of the screen, and that wasn't made invisible.
I do not know if anyone else on these forums or users of Pixelmon want this to be changed, I am just the messenger of those on my server.
(P.S.: Out of all of those who suggested this change, when asked if they would want it permanently swapped for an opaque texture, they said they would not mind if it was an option in the configuration file or if there was a separate .class file to download, etc., in order to provide both a solution for themselves, but also give everyone a chance to choose for themselves which texture looks the best for their client.)