We use an atomistic spin model to simulate FePt-based bilayers for heat assisted magnetic recording (HAMR) devices and investigate the effect of various degrees intermixing that might arise throughout the fabrication, growth and annealing processes, as well as different interlayer exchange couplings, on HAMR magnetisation dynamics. Intermixing can impact the device functionality, but interestingly does not deteriorate the properties of the system. Our results suggest that modest intermixing can prove beneficial and yield an improvement in the magnetisation dynamics for HAMR processes, also relaxing the requirement for weak exchange coupling between the layers. Therefore, we propose that a certain intermixing across the interface could be engineered in the fabrication process to improve HAMR technology further.