The most recent development of the quark-meson coupling (QMC) model, in which the effect of the mean scalar field in-medium on the hyperfine interaction is also included self-consistently, is used to compute the properties of finite hypernuclei. The calculations for $Lambda$ and $Xi$ hypernuclei are of comparable quality to earlier QMC results without the additional parameter needed there. Even more significantly, the additional repulsion associated with the increased hyperfine interaction in-medium completely changes the predictions for $Sigma$ hypernuclei. Whereas in the earlier work they were bound by an amount similar to $Lambda$ hypernuclei, here they are unbound, in qualitative agreement with the experimental absence of such states. The equivalent non-relativistic potential felt by the $Sigma$ is repulsive inside the nuclear interior and weakly attractive in the nuclear surface, as suggested by the analysis of $Sigma$-atoms.
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