The app is often out of date (it's offline and only updated about once per month) and therefore is not a reliable planning tool. It also doesn't limit in any way the trains you can use (some countries are missing completely but Interrail is still valid). If, by the time you're travelling, the train stil doesn't show up in the app, then you can always add it manually.
If a train shows up on a national website, then it exists and you can book it. MÁV now seem to offer online international booking for Interrail reservations (in any case for this train), so by all means book it there.