There is not one single, standard way of treating the vowel extension mark; it can be treated in any of several ways.
The most common method, I think, is to treat it as identical to the vowel sound it represents, and, in the case where there is a word which is spoken identically but contains the actual vowel instead of that mark, order the version containing the mark after.
This style of ordering, using your made-up example words, would look as follows:
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