Perhaps they should return to the station configuration with the twin bridge restored. The Rhymney Railway using Platforms 1 and 2. The Taff Vale Railway using platforms 3 and 4.
In an ideal world with an unlimited budget, yes, this would happen. But as Brissie Girl says below, the project is being done on a finite budget with no room for over-spend.
Not only that, but several buildings either side of the bridge would need to be demolished to claw back railway land lost in the 1980s, including an NCP multi-storey car park, the Cardiff University Trevithick and Queen's buildings, and a more recent massive multi-storey apartment block. In reality, it's just not going to happen. A potential 3rd span across a widened bridge has been mooted over the years but has never come to fruition.
As Brissie Girl also points out, 6tph from the Taff Valley will need to cross the north junction throat anyway to get to the current P2 for the Bay line, unless the junctions are re-configured and Taff Valley tram-trains will be able to enter Queen St from the north into the current P4 and then cross over to get down to the Bay at Queen St south junction when that is re-modelled.
As previously noted, that would increase the project cost considerably, and this is a project with a tight budget. But it is being done, unlike many over the border in England.
And besides, you need half of the Taff Vale services to cross over to the Cardiff Bay branch somewhere so even with four tracks across the bridge it wouldn't eliminate conflicting services.
I would imagine fleet of foot trams will be much more nimble at clearing the junction, especially travelling north from a standing start once they've got the signal to go from Queen St station, than the existing rolling stock.