You want to catch the pcb manufacturing and the bonding with the same layout, is that your goal?
How is the chip mounted to the pcb?
What kind of documentation does the fab that does the bonding need, to get them at the right places and correct sizes?
Does the Gerber format even cater to that?
I don't think PCBnew will be able to create clean documentation for your use case (right now), at least none that would qualify for DRC.