If I'm correct, the version is stored in the metaModelVersion in IWorkingCopyMetaData:
https://apidocs.mendix.com/modelsdk/latest/interfaces/iworkingcopymetadata.html#metamodelversion
And you are right, when you create a project through the SDK, the latest modeler version is used as version, see also this forum post:
https://community.mendix.com/link/questions/88529