If your plan isn't GST registered then yes, you would set your budget based on GST inclusive costs (where they are subject to GST). But your levy contributions shouldn't have any GST included. If your plan isn't GST registered but you are issuing levy invoices as GST inclusive you might want to look at this.
For a GST registered plan, costs that are subject to GST would be budgeted based on the GST exclusive amount. This is because the plan can claim the GST back so it is not actually a cost. Costs that don't have GST (eg water) are just budgeted at their actual cost. GST of 10% is then added on top of the total budget.
So in the case of a non GST registered scheme, for every $1.00 of water you budget you contribute $1.00 with no GST. But for a GST registered scheme, for every $1.00 of water budgeted you actually contribute $1.10 including GST. The 10c GST is lost to the tax office.
