To be honest, I don’t think this is an (undocumented) rule, it’s the TypeScript compiler that’s causing the issue, and there are some modules that provide a workaround (that just doesn’t always work, but that’s not the fault of Athom/Homey).
Besides that, it’s probably possible to get it working for Homey, I just haven’t looked at it very closely.
No maybe not directly, but since changing the outDir or the compiler or even completely removing the build script has not effect, the options are some what limited.