The Bendigo line's bottlenecks are presently on the single-track sections between Kyneton and Bendigo, not between Sunshine and Sunbury. Get those fixed and an actual railway to Melbourne Airport built first, then you can start thinking about linking Tullamarine and Clarkefield.Whilst there certainly are timetable bottlenecks created by the line singling north of Kyneton (anyone who has sat in the Elphinstone Loop for 10 mins + waiting for a cross can attest to this) the situation on the ground is that there are big delays in the Sunshine - Sunbury section.
My regular ride the 5.31 ex Southern Cross normally speeds to Footscray and then makes excellent time till just before Albion where is invariably slows rapidly and then crawls most / all of the way to Watergardens. I haven't made Castlemaine on time in months on that service (which I take 1-2 times per week on average)
Likewise the 09.08 Up ex Castlemaine now makes excellent time till around Keilor Plains where it slows to a crawl and sometimes even stops as it catches up with the preceeding spark. Just before Albion it speeds up again as the spark clears the section and we divert onto the RRL. I don't recall this happening even just a few months ago. It normally makes SC on time though at 10.42 probably due to some timetable padding