There will be three.
Megacouncil will look after local roads and contracting public transport, kind of like ARTA is meant to do now, but doesn't do a good job of local roads. You might reflect on why that is.
NZ Transport Agency will continue to look after the state highways. Ministers don't trust the Auckland Megacouncil to do that. Who would blame them? So the busiest most strategically important roads in Auckland wont be a matter of the Megacouncil.
Ontrack will continue to look after the rail network. Ministers also don't trust the Auckland Megacouncil to do that. Again, key routes for freight (set aside the unprofitable low frequency low density passenger services) are too important to leave to a local authority.
If you want to see how poorly a local authority can perform on transport planning and management you need only look at Auckland's past, which is littered with several planning screw ups. Here are a couple.
1. SH20: Land was designated for the so-called "South Western Motorway" in the 1960s, to link the Southern Motorway to the North Western Motorway. The land was empty at the time, so placing a designation on it meant anyone using the land would know it would one day be acquired for a motorway, so short term leases were the order of the day. However, the ARA and Auckland City Council decided in 1974 that the route beyond Richardson Road to the northwest was not well defined, and so the designation should be dropped from there. As a result the designation only comprises the sections now being built - from the Southern Motorway to Mt Roskill. The Waterview Extension debate is purely because previous Auckland councils decided the South Western Motorway need end at Mt Roskill. Well done. Cost of that decision now runs at least to $1 billion.
2. South Eastern Arterial: Auckland City Council decided in the 1980s that there were inadequate connections between Pakuranga, Mt Wellington and the Southdown areas so decided to revive plans for the "South Eastern Motorway" to link Church St to Mt Wellington Highway and the Pakuranga Motorway, with on and off ramps to the Southern Motorway. It did so on the cheap. The resulting road has few shoulders to accommodate breakdowns, and traffic lights on multiple busy intersections when it should be a proper motorway with flyovers. Ultimately this will need perhaps $100 million of improvements to bring it up to standard to relieve the bottlenecks on this important road.
The Auckland mega council wont change that - and in fact the government doesn't even trust it to manage its own networks.
So let's stop hearing arguments that a single council will be good for transport in Auckland - when there isn't any evidence for that.