For now on Waze will take the Slovenian and other European highway vignettes (toll stickers) into account for routing. \ This changes more personalisation over itineraries across country borders in Europe. You will be able to tell the App that you have a Slovenia vignette and that you also want to avoid other toll roads, getting you full route suggestions via Slovenian highways but avoiding you to have to pay tolls elsewhere.
You can prepare for these vignettes by opening Waze and going to:
Settings > Navigation > Add toll/HOV passes > Vignette SLO - Vinjeta > (Add)