This is a comment on the nature of history and the way history is created and imagined. The English Patient can be read as a form of metahistory, commenting on historical events and personages, but not adhering to the strict structure of 'facts' to make its point.
The study of history, known as historiography, has the scholar consider 'how' history was made, and who the people are who are creating it.
There was some controversy when The English Patient was published. Some people believed it was wrong to 'alter' the truth of history - they felt that it was morally wrong to cast Almasy as a man motivated by love of a woman, as opposed to the various historical and political forces.
Notably, however, Ondaatje makes the point throughout his novel that history is the act of interpretation. In much the same way that Herodotus did, when he wrote his 'Histories', history is no fixed thing - it changes and evolves depending on what evidence is available, who tells the story, who listens - a myriad of ever-changing things. The same story may be told a million different ways, and still be history.
Ondaatje works with universal truths, rather than pure facts in his creation of what is both novel and metahistory. Through reading The English Patient you come to understand the personal struggle that every person involved in the events of World War II must have understood - pain, confusion, loyalty, longing, loss. These are universal themes, and Ondaatje's choice to alter the 'facts', reveals a different way of experiencing and interpreting hisotry.
On of the most well-known historians to publish on historiography is Hayden White. In 1973 he published the seminal Metahistory: The Historical Imagination in Nineteeth-Century Europe. This webpage by Vicki Rae distills White's arguments.