Custom texture location

I would like to use custom textures but the default location is not suitable. I have the system separated in a partition only used for the system so I can’t afford to spend a lot of space with custom textures.

Citra allows you to change the location of the NAND and SDMC. Can I do the same with custom textures?

Not as of currently. What you can do however, is set up a portable Citra build. That way, the entire Citra installation as well as all the user folders would be kept in the same folder and on a drive of your choosing.

To set up a portable build, go to Download Citra - Citra and select Manual download. Then under Nightly Build, click on your operating system’s icon to the right of the latest build available to download the build.
Extract it (.7z can be extracted using Winrar or 7zip) and put it wherever you wish. Inside the extracted nightly-mingw folder, create a folder called user. This Citra should now store all of its config, save files and such inside of this user folder.
Check to make sure that this user folder is in the same folder that contains citra-qt(.exe)
Now run the citra-qt executable found inside of the mingw folder.