If every major language provides an O(n log n) sort function, is it still a leaky abstraction? I'd say no. You can use it without worrying much about the details.
But it sounds like the situation with back-propagation is different, since the internal details of the algorithm affect whether you get a usable answer at all.
A borderline case might be something like a SQL database, where in theory, creating an index shouldn't change query results, but in practice, the performance can change so much that it effectively does.
Unlike with back-propagation, you can tune database performance without worrying about queries returning different results (assuming they don't time out). So it's still a useful guarantee.