Can you, please, come up with some term that would be directly related to geography, but would have no relation to toponymy?
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Google finds two definitions of toponymy, one of which is:
So, any geographical terms not related to place names meet the bill. That said, many of the more common physical geographic terms have been used in place names (hill, mountain, lake, fen, marsh, field, ...), so they're out. More esoteric terms - morraine, perhaps - have seldom been used in place names (at least, in English-speaking countries).
Any geographical terms related to economic geography are relatively unlikely to come under toponymy.