There was a trac ticket requesting improvements to the function since it was inflexible, yet required for themes hosted in official repository. It had been resolved, adding much needed wp_link_pages and wp_link_pages_link filters, so now output can be cleanly modified without need to use custom function.
I went through quite a few takes on this over years and what I have at the moment is Rarst\Hybrid_Wing\Post_Pagination class, which does use new filters but is a little dusty, so might not be comprehensive implementation of Bootstrap markup.
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