The seismocardiogram (SCG) measures the movement of the chest wall in response to underlying cardiovascular events. Though this signal contains clinically-relevant information, its morphology is both patient-specific and highly transient. In light of recent work suggesting the existence of population-level patterns in SCG signals, the objective of this study is to develop a method which harnesses these patterns to enable robust signal processing despite morphological variability. Specifically, we introduce seismocardiogram generative factor encoding (SGFE), which models the SCG waveform as a stochastic sample from a low-dimensional subspace defined by a unified set of generative factors. We then demonstrate that during dynamic processes such as exercise-recovery, learned factors correlate strongly with known generative factors including aortic opening (AO) and closing (AC), following consistent trajectories in subspace despite morphological differences. Furthermore, we found that changes in sensor location affect the perceived underlying dynamic process in predictable ways, thereby enabling algorithmic compensation for sensor misplacement during generative factor inference. Mapping these trajectories to AO and AC yielded R2 values from 0.81-0.90 for AO and 0.72-0.83 for AC respectively across five sensor positions. Identification of consistent behavior of SCG signals in low dimensions corroborates the existence of population-level patterns in these signals; SGFE may also serve as a harbinger for processing methods that are abstracted from the time domain, which may ultimately improve the feasibility of SCG utilization in ambulatory and outpatient settings.