I have just ended a 7 month dispute with my builder and their plumber about the design of my ASHP system. Their plumber is not MCS certified and has no objective qualifications to prove he understands how to design an ASHP system. I wanted an MCS-certified intallation, partly to get the grant and partly to have some peace of mind that the system is properly designed.
I have thoroughly read all of the MCS documents several times. If you take the time to understand what it says, it is clear that a degree of common-sense is required. This is where some MCS-certified designers fail as they just read the basic instructions and use the spreadsheet incorrectly.
My house was built in 1961. The MCS-certified designers my builder approached (MCS umbrella schemes - they design and certify a system for a non-certified plumber to install) all decided that for ventilation rates and room temperatures on the MCS spreadsheet, the house therefore needed to be treated as a pre-2000 construction. In reality my house is a heavily renovated property, designed by a specialist architect to meet Enerphit standards. Therefore it makes a lot of sense to treat it as a new (post-2006) building. This makes a huge difference to the heat loss calculations. This is in the spirit of the MCS standards, which also point the designer to the CIBSE heating system design guide, which itself says that for modern, well-insulated buildings, specialist advice would be advised (rather than making uninformed assumptions).
My architect's plans included detailed u-values for all sections of the building and I know the manufacturer's u-values for the doors/windows, so there is little guesswork required by the designer. The architect's heat loss for my house came out at around 3.9kW (they use PHPP), I got 4kW out of the MCS spreadsheet calculator, two MCS certified companies I approached got 4kW. The two MCS umbrella scheme providers and my builder's plumber all calculated my house's total heat loss at around 8kW.
It all comes down to how carefully you read the instructions, how well you use them and how clearly you understand what you are doing.