I haven't messed with this system in a while or heard anything new about the limit strap routing. There could be news, I just haven't been paying any attention.
I suspect you may be able to make the system work with some fiddling, I just haven't had the urge to get back into it. I've actually been thinking more about doing my own version with less height. Maybe an inch.
It's not flat tires that cause the EAS fault with rods, it's a deflated strut. If you have rods and end up on the bumpstops without the spacers you can push a sensor out of range which will cause the EAS to go red. In that case you need to either use the GAP tool to manually inflate the offending corner a bit to get back in range or use a jack/etc to lift it a bit until the computer will take over again. In theory with the spacer kit you shouldn't have that issue though I've not actually tested this.