Monitoring flowers over time is essential for precision robotic pollination in agriculture. To accomplish this, a continuous spatial-temporal observation of plant growth can be done using stationary RGB-D cameras. However, image registration becomes a serious challenge due to changes in the visual appearance of the plant caused by the pollination process and occlusions from growth and camera angles. Plants flower in a manner that produces distinct clusters on branches. This paper presents a method for matching flower clusters using descriptors generated from RGB-D data and considers allowing for spatial uncertainty within the cluster. The proposed approach leverages the Unscented Transform to efficiently estimate plant descriptor uncertainty tolerances, enabling a robust image-registration process despite temporal changes. The Unscented Transform is used to handle the nonlinear transformations by propagating the uncertainty of flower positions to determine the variations in the descriptor domain. A Monte Carlo simulation is used to validate the Unscented Transform results, confirming our method's effectiveness for flower cluster matching. Therefore, it can facilitate improved robotics pollination in dynamic environments.