Do the Asian highways not use the Jalan Tol? I'm fairly sure that the Trans-Java Toll Road is being built as part of AH2 (and Trans-Sumatra as AH25, etc, etc)
It looks like your routing sources have the JT network of a decade ago, and so those routes take parallel national highways. It doesn't help that these international highways are lists of cities without telling you what way they go between them meaning status quo wins unless signed well (which these aren't - unlike, say, the rerouting of E70 in France away from the unlisted city of St Ettiene and onto the A89 and round the north of Lyon, rather than the south, when the A466 opened).
This lack of update is common with such things - even with stuff like TEN-T in Europe, where corridors are still drawn on their map along national roads despite motorways built with TEN-T money as part of those corridors having opened a considerable time ago and them redoing the lines overlaid on the map about 2 years ago!
I believe the Trans-Kalimantan (already in-browser as AH150), Trans-Suluwesi, Trans-Timor (oddly not anything on other Nusa Tenggara islands, save Bali) and Trans-Papua are Indonesian National Highways without number.
