Lets look at the following scenario.
£100k mortgage, £170k value house
£1m mortgage, £1.7m value house
Both would qualify for a 40% LTV mortgage.
For the £100k mortgage, for the two year term if they were to pay the fee they would pay £10,979 (£9,980 interest, £999 fee) if they were to go with the no fee they would pay £10,380. So they should go with the no fee as it is ~£600 less
For the £1m mortgage, for the two year term if they were to pay the fee they would pay £100,799 (£99,800 interest, £999 fee) if they were to go with the no fee they would pay £103,800. So they should go with the fee as it is ~£3,000 less
I have not included repayments in this (which could be relevant in the end years of a mortgage) and used rates of 4.99% with a £999 fee and 5.19% without fee.
I do agree that for most people, there is likely to be limited difference between the fee and no fee, but wanted to illustrate that there can be a difference.