Positions in an opening can often be reached in a variety of (meaningful) ways, i.e. by transpositions.
When classifying chess games (e.g. in databases or books) by , are there rules or other guidelines which of these transpositions to pick?
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Your question has two different nuances, that is, how to classify an opening and how to classify a game.
The Encyclopedia of Chess Openings' only aim is to classify the first moves of a chess game, it does not concern itself with how the game develops nor further transpositions. Even if a widely known position is reached after an unorthodox choice of moves, the ECO will classify the opening according to these first moves. A comprehensive list can be found both in 365Chess and Wikipedia, the first provides easy access to the variation in question and the second provides the name and some contextualization for the variation.
While the ECO has not an analogous encyclopedia for complete games, the widespread and common way of treating them in the literature is to find the last instance of a known tabiya and consider the game under its umbrella. This ignores the concrete opening, which is often useful since the game may be a relevant addition to the theory on that position, and thus the particular move order leading to it is irrelevant.