. I found strange that Dr. Halliday, on the
chapter about the Portuguese military medical services, on his 1812 book about
Portugal, never calls Ferguson by Dr but always as Mr.

Surgeons were not physicians. Some physicians performed surgery.
While current day surgeons in the UK are educated as physicians, it was not always so. That is why surgeons in the UK are addressed as Mr, Mrs or Ms.

A literary example is Dr Maturin in the Aubrey Maturin series.

Freda Seddon