No, it is as it is and highly unlikely to change, certainly not this summer.
Yes, one of my own first trips-it still was Yugoslavija, was overnight train from Beograd via Sarajevo to Ploce-then bus along coast to Split.
By now there are hardly any trains INTern. to/fro Serbije and none at all to what is now Bosnia/Hercegovina.
Split only has a very few trains direct to Zagreb, in summer season also overnight via Zag to Osijek (near HU border). Buses run up till ev 30 mins in summer.
I have since this first trip also travelled a very few times in Hrvatska, Bosnia, Cerna Gora, Macedonia (and even Albania) and best advice is: go by bus. You are just torturing yourself by relying on trains.
You have to decide yourself if you mostly aim these areas if an IR is worth it-or use one with fewer days to cover the expensive sectors from home (DE? I suppose)-via AT-SLO onward, or maybe also visit other areas. BUS: buy when there, from the busstation. NO, of course not via this IR-app, that should be evident. Learn to use google (do young people even realise nowadays that this exist?) and dozens of busbooking sites will appear-so you can compare. Always best to try to find the operating company then for a booking. And NO-you do not need (it is not even possible) to book that weeks/monthes advance.
Other note: there also used to be a boat line all along the Yugoslav coast-JadroLinija-this has also disappeared.
From Budapest you can use in Summer the direct Nighttrain to Split :)
Budapest - Belgrade best to go by bus or minivan transport
Belgrade - Sarajevo - Split Buses or by rail to Montenegro (Have a look on Bay of Kotor ) and then from Montenegro by Bus to Sarajevo then the scenic rail line down to Mostar and finally by Bus to Split From Split you have trains to Zagreb (all year) , Budapest,Vienna,Graz,Bratislava,Prague (in summer as Nighttrains)