It makes him seem shorter? This isn't right. The painting is larger than real life so Henry does not seem short.
It's not right to say that it makes no difference either. Holbein was very careful what he put in his paintings.
The correct answer is that it makes him seem above the viewer. Henry was the most powerful man in England. He was socially 'above' everyone else. This step also makes him physically above everyone as well. He is looking down on his people.