I would rather remove the $identifier altogether, or stick it to the end of parameter list, with default value, in all cases.
Most of the query calls do not use it, so forcing the addition of an empty parameter at the beginning of the parameter list doesn't make much sense to me.
That said, no qualms here, to a temporary inconsistency.

Most of the query calls do not use it, so forcing the addition of an empty parameter at the beginning of the parameter list doesn't make much sense to me.

You mean like was done with
$smcFunc['db_query']('', 'stuff' ,array(more stuff)) 👼

I would rather remove the $identifier altogether

So don't use substring in my query and loop on all the rows with php? Or was that a general statement to the 99% unused leading parameter in our smcFunc calls ... as in don't do that again even though its consistent and leave the $identifier as I did in the upgrade script?

I'd remove $identifier from smcFunc['db_query'] thing. So well, it's fine as you did, IMHO there is no need to try to adapt upgrade_query() to have the parameter first in the list, since we can consider this signature deprecated. (it might remain or not - depends on time - for 1.0, but it's still deprecated.)

OK ... I'll close this for now since I'll have to rewrite how it updates custom fields to not use substrings in the query ... that will be a bit of a mess really but I'll deal with that once I know what upgrade_query is going to become