According to the Prime Minister in Question Time today, the Ministry of Justice has already advised that based on the 1999 experience, holding a referendum at the same time as the election would lead to severe logistical problems, voter confusion, and a delayed count. This would not be a problem with sufficient lead time, but they would have had to have started around April to get it done properly. So instead they've recommended that any referendum be held by postal ballot sometime next year.
I am endeavouring to get a copy of the advice ASAP.
Update: I should add: according to MoJ, a referendum would cost $10 million whether it was run concurrently with the election or not. So the financial argument used by some to justify running it as quickly as possible is simply bogus.