You can use the trains of the participating companies. Whether these trains are indicated on a map or shown in the planner app, is not relevant.

You can practically take like 95% of the trains in Europe with an Interrail pass.

The most important/popular /visible trains that are not included are those operated by RATP, some smaller private train companies (like Flixtrain, Italo) and some touristic railways (usually high up in the Alps, south of Interlaken like BOB, Jungfraubahn,...).