Recent anisotropic flow measurements in and collisions at a center-of-mass energy per nucleon pair of 5.36~TeV provide evidence for nuclear geometry-driven collectivity. In this Letter, we investigate the femtoscopic signatures of nuclear geometry in these light-ion collision systems, using a hybrid simulation framework that couples nuclear configurations to viscous hydrodynamics and hadronic transport. We show that the ratio of the freeze-out eccentricity, extracted from azimuthally sensitive femtoscopy, reaches 1.5-1.8 in central collisions for deformed nuclear configurations, compared with about unity for a spherical baseline. This enhancement is significantly larger than that of elliptic flow in the same simulations, and remains stable when pre-equilibrium free streaming is omitted, even though the absolute source radii change considerably. Confronting these predictions with future data will provide new, complementary constraints on nuclear structure and initial-condition modeling.

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