I have an engine registering a preprocessor for its own template files. It receives all templates for routes but none of the templates for components.
The route templates are co-located with the route js files by setting the podModulePrefix.
The component templates are co-located with the component js files using standard component location.
The above configuration works for apps and engines otherwise, but could be part of the trouble here. I'd note though that addons that add a preprocessor for the engine get access to both, so I suspect the issue is elsewhere.