No, it's *not* a fair system! In a system largely controlled by TRVs, simply recording the zone valve's 'on' time provides a very inaccurate measure of the amount of energy consumed. It won't distinguish, for example, between freezing cold days when the heating is running full chat and mild days when the TRVs are closed for most of the time.
If you feed the shop central heating off the house gas supply you can pay for domestic gas supply at 5% VAT. If the shop has its own business gas supply it'll be VATed at 17.5%. One big bill will also likely be cheaper on a per-unit rate than two smaller supplies.
This may of course depend on whether your business is VAT rated and how you apportion the expenses for your business accounts.
Owain
For this sort of setup charging a flat all inclusive rate for heating&water makes a lot more sense. Electricity is similar, unless you separate out each room's supply.
If there is no gas in the property, you could consider an alternative.
What about an Air Heat Pump. These work best in properties that are well insulated but can save a lot of running costs and can produce hot water as well.
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