Optical cavities can induce photon-mediated interactions among intracavity-trapped atoms. Multimode cavities provide the ability to tune the form of these interactions, e.g., by inducing a nonlocal, sign-changing term to the interaction. By accounting for the Gouy phase shifts of the modes in a nearly degenerate, confocal, Fabry-Perot cavity, we provide a theoretical description of this interaction, along with additional experimental confirmation to complement that presented in the companion paper, Ref. [1]. Furthermore, we show that this interaction should be written in terms of a complex order parameter, allowing for a U(1)-symmetry to emerge. This symmetry corresponds to the phase of the atomic density wave arising from self-organization when the cavity is transversely pumped above a critical threshold power. We theoretically and experimentally show how this phase depends on the position of the Bose-Einstein condensate (BEC) within the cavity and discuss mechanisms that break the U(1)-symmetry and lock this phase. We then consider alternative Fabry-Perot multimode cavity geometries (i.e., beyond the confocal) and schemes with more than one pump laser and show that these provide additional capabilities for tuning the cavity-meditated interaction among atoms, including the ability to restore the U(1)-symmetry despite the presence of symmetry-breaking effects. These photon-mediated interactions may be exploited for realizing quantum liquid crystalline states and spin glasses using multimode optical cavities.