It should be relatively easy for you to measure the length of the external walls of your home.
Then deduct the cavity wall thickness which will be 250mm to 300mm (you can measure the wall thickness by opening a window)
You will then have an A x B = square metres. Multiply this by the number of floors and you have the accurate total area of your new home.
It is hard for me to believe Persimmon would be so stupid to advertise your home as a certain total area and it to be less than stated as this is a serious breach of many regulations and would have very serious consequences for the company.
However, all housebuilders state a "tolerance" of usually plus or minus 50mm for each room dimension stated. Even so, this is unlikely to result in the discrepancy of 140sqm in the brochure, to 138sqm on the EPC.
Regarding Persimmon submitting details for Council Tax purposes, I can only assume this was used for business rates, such as an ex-showhouse, sales office, or a stock unit (completed for three months or more). As the Council Tax is determined by the Valuation Office and this assesses what "value" your new home would have been in 1991 to assign a Council Tax Band. You can of course challenge this. The "valuation" has nothing to do with the total floor area as far as I am aware.