But you'd imagine there would be the appropriate software available to minimise the time taken to provide this.
Nah, that's not the problem. It's the fact that you have to check, reconcile, balance, verify.... or basically go over every single with a fine comb. It's not like business services where you only check or reconcile the highly material accounts.
I can't rely on your spreadsheet. It is not third party documentation.
The processing is cake. The workpaper file for the auditor (and of course for the ATO if they even want a sneak peak) is where the fun begins. The compliance review checklists are tedious. We have to do minutes and "cover your ****" pieces of paper for every small thing now. If you don't have them the CPA or CA generals come wandering into your office come compliance audit time and tell you to fix your processes. The legislation and ATO regulations are so damn convoluted that is necessary. All of this was made clear to you when you signed the trustee declaration and read the "welcome to life as a SMSF trustee" package the ATO gives out and papers all over their site.
The average accounting firm will only have an SMSF fee base of $500k-1 mil per year. In most cases it could be a lot less. 40% of this will be taken up in overheads. To get accounting software that is not full of what I would consider technical issues you would be paying in excess of $50,000-$100,000k a year. The small firms, because this is a specialist industry now, will probably not realise there are too many technical issues, but they may find that the software often does strange things. A small show isn't going to afford highly sophisticated software because the scale is just not there.
The whole industry is a joke - I said the fee seemed reasonable considering what the industry charges, not that I actually think it's fair. I actually feel insulted by the OP, considering I probably earn less than he does.
If you think you are being charged too much by the industry buy a single user software license and do it yourself. Then go down the road to your friendly two-bob auditor and get the thing signed off. Actually it pisses me off that you don't - because I have to deal with smart arses like you day in and day out.