I think there are five possible reasons:
- the construction meant a limited choice for possible letters and some of the three-letter words did not lend themselves to good clues;
- it's a way of defeating those who use sites like Quick Solve without solving the clue;
- because some of the letters are unchecked, the clue has to be fully solved;
- it provides an additional challenge;
- Miles seems to like the twists: for example, he often goes for less common definitions.
Or maybe I'm missing something.
Extending this approach to longer words would make an interesting future puzzle.