The Borromean $^6$He nucleus is an exotic system characterized by two `halo neutrons orbiting around a compact $^4$He (or $alpha$) core, in which the binary subsystems are unbound. The simultaneous reproduction of its small binding energy and extended matter and point-proton radii has been a challenge for {em ab initio} theoretical calculations based on traditional bound-state methods. Using soft nucleon-nucleon interactions based on chiral effective field theory potentials, we show that supplementing the model space with $^4$He+$n$+$n$ cluster degrees of freedom largely solves this issue. We analyze the role played by the $alpha$-clustering and many-body correlations, and study the dependence of the energy spectrum on the resolution scale of the interaction.