Whatever happens, I would be extremely surprised if the railway crossed the NSC at ground level with roads both below and above. The practicality of having the Cross Road intersection at anything other than ground level rules it out.
The NSC is inevitable, but I do see it turning into a political project in terms of one major party preferring an elevated motorway while the other prefers the motorway in a trench, and the party in power at the time getting their choice of strategy. Both main parties in SA agree completely on having rail as a low priority in any respect other than shoving it out of the way for road traffic, so DPTI will have no choice but to rebuild the railway around whatever gets chosen as the headline priority for the motorway.
If the railway was a priority in the project, then it would result in the North-South Motorway being sunk, the intersection between Cross Road, South Road and the motorway ramps at surface level and the railway over the top. It would be the method of least disruption for the railway, just like the bridge built over the T2T section of the NSC with just weekend works and one short shutdown for the heavy lifting. The optics are better too, it's good for motorists to see public transport cruising overhead while they are stuck in a traffic jam.
I think it's fanciful to suggest the line will turn right after Raglan Ave to head through the former Hills site, left to straighten up and then turn right again to point towards Clarence Park station. You won't be able to make things faster by replacing two curves with three in the same space.