I don't think relying on having not bottomed out yet is a good idea, unless you have been riding that way for years (sounds like you have not). In the last year I bottomed out twice.. two times too many for me. I didn't get a flat either time but I did warp my brake disc on one hard hit and was probably not far from rim damage. I eventually realized my pump was mis-reading and no bottom-out since I corrected for that.
If you are regularly on rough pavement I would fit the biggest most supple tires you can, set up tubeless for added insurance against pinch flats, and run a bit on the low side of the recommended pressures (say 5-10psi below the SRAM calculator which itself seems lower than the Silca one).