However, the geographies simply don't match. This was the result not so much of a deliberate decision on Tolkien's part to have things so but rather a side-effect of the history of the composition: the question did not occur to him until the story was too far advanced and the map too fixed to allow much alteration:
... if it were 'history', it would be difficult to fit the lands and events (or 'cultures') into such evidence as we possess, archaeological or geological, concerning the nearer or remoter part of what is now called Europe; though the Shire, for instance, is expressly stated to have been in this region [FR, 11]. I could have fitted things in with greater versimilitude, if the story had not become too far developed, before the question ever occurred to me. I doubt if there would have been much gain; ... Letters, 283 (#211)
... As for the shape of the world of the Third Age, I am afraid that was devised 'dramatically' rather than geologically, or paleontologically. I do sometimes wish that I had made some sort of agreement between the imaginations or theories of the geologists and my map a little more possible. But that would only have made more trouble with human history. Letters, 224 (#169)The remark that there probably would not "have been much gain" is characteristic and perhaps indicates Tolkien's own approach, which would seem to have been to focus on the environmental familiarity at the "local" level (in the sense that any particular scene might have come from somewhere in Europe) and to simply overlook the lack of "global" identity. On the other hand, he made some attempt to address the difficulty in the quote from the Prologue (FR, 11), where it was said: "Those days, the Third Age of Middle-earth, are now long past, and the shape of all lands has been changed...". The conclusion is that it is a matter for each individual reader as to how important is the lack of geographical fit and where one comes down on the continuum between "Middle-earth was northwestern Europe" and "Middle-earth might as well have been northwestern Europe" (or, as Tolkien might have said, "Middle-earth 'imaginatively' was northwestern Europe"). [Thus, recent attempts to force the M-e map to fit the map of the Eurasian land mass, such as in Tolkien: The Illustrated Encyclopedia by David Day, should be discounted.]
In one letter he provided indications to help in visualizing the circumstances of various locales, but this does not help in resolving the above matter, since again northwestern Europe was used for comparison rather than equation:
The action of the story takes place in the North-west of 'Middle- earth', equivalent in latitude to the coastlands of Europe and the north shores of the Mediterranean. ... If Hobbiton and Rivendell are taken (as intended) to be at about the latitude of Oxford, then Minas Tirith, 600 miles south, is at about the latitude of Florence. The Mouths of Anduin and the ancient city of Pelargir are at about the latitude of ancient Troy. Letters, 375-376 (#294)