That sounds like quite an over-complicated structure, lots of overlap (e.g. it seems that roads and ports are no longer transport infrastructure, it's not clear whether projects like Melbourne Metro are infrastructure or public transport) and lots of opportunity for dodging accountability.You have to remember that the delivery agencies (LXRA, RPV, West Gate Tunnel, North East Link, Major Road Projects) have been operating separately from Transport for Victoria (V/Line, VicTrack, VicRoads, port regulator, and so on) for several years now. I said a while back it is working quite well and to me it makes sense to have the ministerial structure reflect that.
A clearer structure would have a single Minister for Transport and Infrastructure plus a couple of non-ministerial 'spokesperson for xyz.'
It looks to me like at least one of them is being set up to mainly serve as a sacrificial lamb when things go wrong. Horne would be the most likely candidate, as a newbie MP in a seat so safe that even a donkey wearing a red ribbon could get a 65% vote.
Using your example, Metro Tunnel is being delivered by RPV so clearly Minister Allan's responsibility.