The long injection segment (flat bottom, FB) of the cycle in the Super Proton Synchrotron (SPS) used for filling the Large Hadron Collider (LHC) with Pb ion beams exhibits strong beam losses and transverse normalized emittance ϵx,yn growth. During the 2024 run, significant beam transmission improvements enabled record intensities delivered to the LHC, mainly leveraged by operational measures such as working point optimization and compensation scheme for the 50 Hz ripple from the main quadrupole power converters. This paper summarizes these improvements, and presents recent advancements in particle tracking simulations of the SPS flat bottom, including effects such as space charge in the presence of tune modulation induced by power converter noise. These simulations are compared with measured beam parameters in various scenarios, followed by a discussion on the relative importance of each effect and their estimated impact on the CERN ion programmes.