Seriously, is there no route of appeal?
I deleted the sarcasm again!
Nope.
SEPA (and others) may well object at the Outline or Detailed planning stages, and do.
However, SEPA are consulted at the Building Warrant stage. This is
after the planning process (complete with right of appeal, all the way up to Wee Eck himself). Whilst the extension could have gone ahead, SEPA used their authority to insist upon a sewage treatment plant costing tens of thousands being installed. This in itself would require planning permission.
The same thing happened to me. The septic tank was installed in the 1950's to serve 20 persons and now serves two. It was updated to exceed current effluent standards. When I planned the new house, all went swimmingly through planning. I was demolishing a three bedroom house and replacing it with a two bedroom house pretty much on the same footprint. When it came to the Building Warrant stage, SEPA insisted on my demolishing the old septic tank and replacing it with a plastic one with a capacity for five persons. I was also required to pay them a one-off fee of ?70 for a licence to discharge. The good news is that I could do this online. I just had to mark a cross on an online map the discharge point of my tank. The scale of the map means that my cross was 100 x100 metres wide!