Positivism will get you really far, and we have not tapped some of its most powerful insights.
Modernism is full of people who consider all of metaphysics either decided or irrelevant. My favorite one of these alive right now is Daniel Dennett. He thinks that we need to take science and apply it to our philosophy, deconstructing problems we don't realize are already solved, which decides, and then removes large areas of metaphysics. This is an entirely positivist endeavor.
For instance, he is most famous for working from the known structure of the brain, and realizing that it means the 'Cartesian Theater' with a centralized self observing outside reality was not an option. Whatever strong metaphysical attachments we had to the self, it was optional, and all the thinking around it needed to be used to pull it apart and generate a theory of self congruent with the parallel and distributed nature of neuronal processing.
On the other hand, hard-core modernism is dead: We know positivism fails. We see that it ultimately fails as an basis for truth through modern logical analysis. And we see it fail as a strategy for dealing with reality on a regular basis by looking at history.
Late modernist historians of science like Kuhn pointed out that can proceed with a positivist endeavor only by freezing a given set of metaphysical assumptions. No progress is possible if you have not already made decisions about what is and is not real, knowable, etc. Whether or not you have expressed those, you have to be working from the same basic notions. When theoretical explanations of observed results cannot fit into those presumptions, for instance the idea that there is a fixed global frame of reference to which all events are equally related, you have to rewrite parts of that provisional paradigm.
This is itself a defense of the relevance of metaphysics. You cannot discuss alternatives to such propositions if you do not have a fund of metaphysical analysis from which to draw distinctions and propose alternatives. The only place to get ideas and habits you need to talk about the things that up until now were wholly outside of your physics from the possibilities we have entertained about those things that currently appear wholly outside physics in general.
Atomism went from metaphysics to physics when chemistry demonstrated that chemical transformations involved small fixed and generally integral ratios of masses. Until then, it was impossible to decide, because we lacked the right kind of problem. If it had not existed as a metaphysical concept already, we are unlikely to have come up with it at the right time.
And Kant's Antinomy of Atomism motivated us to not trust it too completely, and to reach behind it looking for continuous descriptions of the apparently discrete reality. We know that there is a deep paradox here, and we are not shocked that we come down to some weird partially discrete, partially continuous solution. We expected that -- we just didn't realize it.
That we can expect these things to change faster and faster as we watch cultural development accelerate implies that we will be making use of a lot of metaphysical ideas that we currently don't care about. The fact that we do not have leverage on problems that make the concepts relevant right now, does not mean we will not need those concepts.
So metaphysics is generally not justified in its conclusions, but it is justified in analyzing and expanding different ways of looking at the kinds of explanations people can reasonably make and share about abstract reality, ultimate truth, etc. Some of them will have such major flaws they can never be redeemed. Others will interact and generate more options.
The same way that mathematics provides the power behind ordinary, everyday science -- what Kuhn calls the 'normal science' of 'puzzle solving' -- philosophy often provides the power behind resolving paradigm shifts and other arguments of crisis throughout scientific history.