Is it possible to have Altium ignore one schematic in a project?
The best option to resolve that doesn't imply to manage the build configuration, if just to use the file manager.

Right click on the project add existing file

Right click on the file remove from project. 

Therefore you can compile the file you want. It only take few seconds and it works. But if you really need to make custom configuration. You should contact AD support throught the support center in Help tabs. 

Regards MathieuL.