We study bounded operators defined in terms of the regular representations of the $C^*$-algebra of an amenable, Hausdorff, second countable locally compact groupoid endowed with a continuous $2$-cocycle. We concentrate on spectral quantities associated to natural quotients of this twisted algebra, such as the essential spectrum, the essential numerical range, and Fredholm properties. We obtain decompositions for the regular representations associated to units of the groupoid belonging to a free locally closed orbit, in terms of spectral quantities attached to points (or orbits) in the boundary of this main orbit. As examples, we discuss various classes of magnetic pseudo-differential operators on nilpotent groups. We also prove localization and non-propagation properties associated to suitable parts of the essential spectrum. These are applied to twisted groupoids having a totally intransitive groupoid restriction at the boundary.
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