I understand what a microdot actually is, but how did spy agencies create text that small with the technology from the 1940's? What was the process that spies used to create the microdots from wherever they were located, since they would not have the facilities available to headquarters?
There were (and are) many methods of making microdots, and they didn't necessarily require resources any more unusual than with ordinary photography. The 'British Method' is one simple example; a high-contrast black and white photo of a document would firstly be taken in such a way that the document filled the whole frame of the film. The film is developed as per normal, and the negative was mounted in hole cut in a piece of black cardboard. When lit from behind, with lamps, the text on the negative was visible very clearly in black and white. This image was then photographed from a close distance to produce a c. 1mm length image, which was then cut out to make the microdot itself.
This was a more clunky process than later systems such as the KGB's 'Bagulnik' system but it was still quite simple.
Here is a picture of a reconstructed process from Melton.
Source and further reading
H.K. Melton (2002, revised from previous ed 1996), 'Ultimate Spy'. Dorling Kindersley. See esp. pp 150-153.