We discover unexpected connections between packing configurations and rare fluctuations in dense systems of active particles subject to pulsation of size. Using large deviation theory, we examine biased ensembles which select atypical realizations of the dynamics exhibiting high synchronization in particle size. We show that the order emerging at high bias can manifest as distinct dynamical states featuring high to vanishing pulsation current. Remarkably, transitions between these states arise from changing the system geometry at fixed bias and constant density. We rationalize such transitions as arising from the change in packing configurations which, depending on box geometry, may induce highly ordered or geometrically frustrated structures. Furthermore, we reveal that a master curve in the unbiased dynamics, correlating polydispersity and current, helps predict the dynamical state emerging in the biased dynamics. Finally, we demonstrate that deformation waves can propagate under suitable geometries when biasing with local order.