I would like to start using Altium to simulate parts of my schematic, but I would much rather have a separate "simulation schematic" inside the project which should be annotated and compiled independently to the rest of the schematic sheets inside the project, Is that possible ?
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.