I think it would probably be more of an opportunity than an annoyance, because more of the preserved railways will run on weekdays than they normally do.
I don't know much about preserved railways in the other states, but Steamranger only see a surge in school holidays on the Cockle Train because it's the perfect length for families (30 minutes each way) with their longer trains being no different to normal. Pre-booking for the Southern Encounter is a must all the time, Sunday 4 October will be no different to normal just because of the school holidays.
The National Railway Museum (located at Port Adelaide) sometimes puts on extra events and activities for families during the school holidays, but nothing is shown for the October school holidays other than the Port Festival on the 10th/11th when their heritage diesel railcars will run on the mainline and the museum will have free entry. The NRM is open on most public holidays, so you could do that on Monday 5 October (Labour Day public holiday).
The Overland takes a full day to cover Adelaide-Melbourne and runs twice a week in each direction, Monday/Friday to Melbourne and Tuesday/Saturday to Adelaide. This could be a good one to do from Melbourne to Adelaide on Saturday 3 October, before doing the Southern Encounter on the Sunday, then on the Monday the National Railway Museum and perhaps a trip to the Adelaide Hills (to see 1500 metre long freight trains working hard on a 2.2% grade) before flying on towards Perth after that.