- The writer should have taken care not to hide such a (relatively) obscure meaning underneath an obviously silly one.
Could the indefinite article "an" be used here, instead of "a"?
The answer is no, that it should be an "a".
The choice of the article--"a" versus "an"--happens to be the only systematic exception to the general rule that a parenthesised element doesn't affect the grammar of the sentence.
Related info in a vetted grammar source, the 2002 CGEL on page 1748:
In their primary use parentheses occur in pairs and enclose what we will call a parenthesised element. Their function is to present that element as extraneous to a minimal interpretation of the text, as inessential material that can be omitted without affecting the well-formedness and without any serious loss of information. [fn 16] . . .
footnote 16: The only systematic exception to this generalization is that when the indefinite article precedes a parenthesized element its form (as a or an) depends on the properties of the first word within the parentheses: She made an (interminable) movie about a (supposedly endangered) owl. The choice between a and an is made on a phonological basis (see Ch. 18, &6.4), and always on the basis of the sentence as it would sound if read aloud with the parenthesized element included.
Note that 2002 CGEL is the 2002 reference grammar by Huddleston and Pullum et al., The Cambridge Grammar of the English Language (CGEL).