This happens because Syside loads two copies of the standard library - one is bundled together with Syside. Path to standard library can be changed with "syside.stdlib": "path/to/sysml.library" configuration option, or you can exclude paths/globs with "syside.exclude": [...] configuration option. Note that at the moment Syside expects standard library to be under a single directory, e.g. sysml.library, and using a custom standard library may show diagnostics.
We are working on full integration with Sysand and model dependencies.