Methods, apparatuses and systems in an integrated bonding system for optimizing bonding alignment between dies and a substrates include bonding, using a bonder of the integrated bonding system, a first die to a first substrate using preset alignment settings, transferring, using a transfer arm/robot of the integrated bonding system, the bonded die-substrate combination to an on-board inspection tool of the integrated bonding system, inspecting, at the on-board inspection tool, an alignment of the bond between the die and the substrate of the bonded die-substrate combination to determine a misalignment measure representing a misalignment of the bond between the die and the substrate of the bonded die-substrate combination, determining from the misalignment measurement, using a machine learning process, a correction measurement to be communicated to the bonder, and bonding, in the bonder, a different die to a different substrate using the determined machine-learning based correction measurement.