I think the business case kinda gold plates the electrification to Baxter options which obviously bumps up the price, with little extra benefit.Includes all of the grade separations and a large stabling yard, also would need costs to relocate the freight and passenger trains on the stony point line too, the costs would start to add up. Mernda line about the same length was about 600 million (very little disruption to existing network and small stabling yard), and Cranbourne line duplication around 700 million (with grade separations in comes about the cost of 1-2 billion dollars).
If you consider the above post and this post then why would anyone want to invest $1.5b in the proposed upgrades which will never deliver more customers anyhow? The issue is clear to me, rail services are so bad on that line people are voting with their cars and not using it as much as they should or rather could.
The business case needs to forget about grade separation for a semi rural area and electrify to Stony Point and then with key loops at stations (like those in other single track sections) increase frequencies. No wonder the place is a mess in PTV.
If you reduce the stabling yard to a smaller facility, just grade separate the busiest potential crossing plus no expensive station rebuilds then it would seem really viable.
Anyways this is just the "premilinary" business case, the true business case would evaluate it further and probably find more economically viable options.
1.5 billion to Baxter is definitely less viable, than the combine Mernda and Cranbourne upgrades, due to they are being in growth areas as well as good development opportunities at Mernda town centre and revitalizing Cranbourne town centre.
I don't think there's a need to electrify the whole Stony Point line, it's a rural branch line, although extending the electrified network past Frankston is a possibility. Honestly the regional rail lines like Geelong, Ballarat and Bendigo would probably be better off electrified first before considering the whole length of the Stony Point corridor.