I've been submitting CIC accounts in the same format for the last 8 years and they've always been accepted by CH.
This year they have rejected them as the statement "These accounts have been prepared in accordance with the provisions applicable to companies subject to small companies regime" was in the directors report (where it's always been for the last 8 years) not below the balance sheet.
My fellow director submitted the accounts in December before going away on holiday so didn't get the letter saying they'd been rejected until after the deadline so we will get a penalty fine of £150.
My theory with CH is that they only go to this level of pedantry if the accounts are near a deadline particularly before Christmas so they can generate these fines which pay for their existence (£70M in fines a year I've heard).
However I have discovered that if a set of accounts was accepted in previous years in the same format then an appeal against the penalty will be successful. If we get fined I'll appeal and let you know the outcome.
I totally agree with your theory...I have had charitable companies similarly rejected over the Christmas period and hae succesfully appealed on the grounds that it is reasonable to expect that if they have accepted them in a format that is the correct format for Companies House. Good luck! I have had many struggles with Companies House and have succeeded in getting compensation from them! They are in the habit of writing to CICs, charities etc saying they can file online when they are prohibited from their own legislation from doing so.