I think a big part of the issue is that - because of the way Haskell's cross-module inlining works - you need to generate different artifacts not just for each version you use but for each set of dependencies chosen for each set of flags set for version you use. I think this strips away much of the benefit of the second approach.
Part of the benefit of backpack seems to be that you can compile modules separately from their dependencies and if this is correct it should go some way to addressing the issue you raise.
