"you need to get your antenna rule checker to not complain about missing substrate diodes"---But the antenna rule checker only cares whether or not there is diffusion connected to the net or not. You only need to satisfy antenna violations inside your analog block. It is always useful to consider how a parent cell is going to route wires to your analog block, so where you have sensitive inputs (i.e., input goes only to a FET gate, with no direct path to diffusion) it is always a good idea to stick in a diode to mitigate the possibility of antenna violations. You cannot anticipate everything that will be done in the parent cell to route to your block, but you can make it less likely for violations to occur.