No one saying it wasn't designed for future track amplification. But let's compare like for like.
I was involved with Wyndham Vale station a decade ago. The design allows for Metro platforms and interchange with stabling built alongside and not affecting the Geelong line. A lot of excavation in rock but doable unless someone has sold off the land
Werribee to Sunshine and Werribee to Newport there is ample room for additional tracks at little extra expense (ie no massive earthworks needed outside of station precincts).
Sunshine to Spencer St and Newport to Spencer St will both require tunnelling or heavy earth words for track amplification.
Manor Junction to Sunshine: ~35km of greenfield (cheap) construction
Sunshine to Spencer St: ~12km of Tunnel (expensive) construction
Manor Junction to Newport: ~25km of greenfield construction
Newport to Spencer St: ~8km of tunnel construction
Option 2 seems to be the cheapest option. RRL was cheaper than Option 2 because it tacked onto the exsisting Ballarat and Bendigo Lines, but now they are at capacity and there isn't as much room for cheap greenfield construction