I think you underestimate the effect of 'than' in the sentence, but with 'than' the sentence is no longer a classical conditional sentence like:

migrants would still be better off if they stayed at home.

With 'than' it's a comparison of two situations (scheme: A is ..er than B): a real one (even if yet to come) and a no longer possible one ('if they had stayed' - no longer possible; 'if they stayed' - still possible). That's why the rules for classical tense combinations in conditional clauses don't have to be observed. The if clause is an isolated statement about a no longer existing possibility.

The use of past perfect in the if clause clearly states that the sentence is about already arrived migrants, for whom the option to come or to stay no longer exists. Another support for this view is 'migrants will be better off'. 'migrants' have already migrated, not so 'possible/potential/prospective migrants'.

I think you underestimate the effect of 'than' in the sentence, but with 'than' the sentence is no longer a classical conditional sentence like:

migrants would still be better off if they stayed at home.

With 'than' it's a comparison of two situations (scheme: A is ..er than B): a real one (even if yet to come) and a no longer possible one ('if they had stayed' - no longer possible; 'if they stayed' - still possible). That's why the rules for classical tense combinations in conditional clauses don't have to be observed. The if clause is an isolated statement about a no longer existing possibility.

The use of past perfect in the if clause clearly states that the sentence is about already arrived migrants, for whom the option to come or to stay no longer exists. Another support for this view is 'migrants will be better off'. 'migrants' have already migrated, not so 'possible/potential/prospective migrants'. Yes, the text is about a general situation, but about the general situation of migrants in their new country - not about the general situation of potential migrants in their original countries.