I think that the current proposed alignment is the correct one. But I think it should be connected at its Sunshine end to the RRL and not the Metro network. Also, it should continue past the airport (perhaps up the median of the proposed extension of the Tullamarine Freeway) to a (very) large triangular junction with the (broad gauge) railway down the middle of the proposed Outer Metropolitan Ring Road. There should be a connection between that railway and the line to Sunbury and beyond.
This would allow V Line trains towards Bendigo and Seymour to also serve the airport. An off-peak 10 minute frequency at the airport could be achieved by running trains every 30 minutes to Bendigo (express to Kyneton), every 30 minutes to Kyneton and every 30 minutes to Seymour. (Yes, I know there'd need to be reduplication beyond Kyneton.) Those trains would also avoid any conflict at all with the Metro network (if there was also quadruplication between the OMRR and Sunbury).
I don't think that passenger volumes to and from the airport would be so great as to crowd out longer-distance passengers. Also, passengers to and from the airport would get the benefit of trains with luggage racks.
I also think that any airport service should be charged at a premium rate, which is sustainable given how expensive the "competition" is. (Airport workers can be rebated like they are at Heathrow.) This would also be necessary to avoid passengers from Sunbury and Wallan crowding the trains in hopes of a quicker, express journey to the City. I think this could be done by making the airport station a new zone, call it "2A". It could be charged at the zone 2 rate plus a surcharge of $X. Passengers could use the V Line trains between the City and Sunbury / Wallan but the surcharge would be added when the conductor checks their tickets or when they touch off.