For $G$-spectra in the sense of Gaunce Lewis and myself, and therefore for the $S$-modules of EKMM (Elmendorf-Kriz-Mandell-MayElmendorf–Kriz–Mandell–May) use of a universe is truly essential: $G$-spectra are obtained from $G$-prespectra as colimits over inclusions of sub $G$-inner product spaces of a universe. Such colimits make no sense without use of some device to ensure smallness. In this line of development, use of a universe seems truly essential. The linear isometries $G$-operad $\mathcal L$ is central to the construction of the smash product (and to lots of work in equivariant infinite loop space theory), and $\mathcal L(j)$ is the $G$-space of linear isometries $U^j\to U$, where $U$ is the universe in which one is working. It would be ludicrous to try to make sense of that without working in a universe.
As a philosophical point, it is essential to be eclectic in this area and to allow use of different categories of $G$-spectra, such as orthogonal and Lewis-MayLewis–May or EKMM, since there are many things that one can readily prove with one and not the other. For a comparison of these two and discussion of change of universe, see for example Mandell-MayMandell–May, Equivariant orthogonal spectra and $S$-modules.
That source explains how, in orthogonal $G$-spectra, one can actually work with one fixed universe, even the trivial one, and obtain equivalent categories as Tyler says. Hill-Hopkins-Ravenel Hill–Hopkins–Ravenel took that observation from Mandell-MayMandell–May and ran with it. To be honest, I sometimes regret we made that observation; as Tyler notes, it can be a source of confusion, and it can sometimes obscure the mathematics. Here again it is wise to be eclectic and think in terms of both physical change of universe and “phantom” change of universe in terms of that observation.