Not neccessarily, if he bought a new van for £20k and new equipment for £20K, then Annual Investment Allowance may well turn his accounts profit into a loss.

So if for instance he draws dividends of £28,000, salary of £9,000 and receives interest of say £7,000 - HMRC software will calculate his 2017-18 liability to income tax at £1,737.50, whereas the correct liability is £125 less at £1,612.50 .

There is insufficient information to allow that conclusion.
If his company has made a profit there will be corporation tax to account for as well.
If his company has not made a profit it is possible that HMRC would look at his receiving a dividend of £28,000 as not being in line with the company's position, and as such the structuring as a company is being used as a method of avoiding paying income tax.

In matters of Income Tax, as with VAT, I would suggest people refer to HMRC for details of the correct calculation, as stated by Bozo in an earlier discussion: I would suggest that folks refer to HMRC VAT notices before giving "man in the pub" opinions which are wrong.