To me Z14 is too complicated. Too many switches for configuration, but if that is what you have then I think the intent from looking at Z-27 or Z-28 is that the electronic ignition run from the Battery Bus. I see what you are getting at about if you loose your primary battery you will lose one ignition. I think you are correct.
I think there are other ways of doing it, but it really depends on how many of these cross-feed relays and control switches you have, and exactly how you wired up your setup. It would appear to me that you could put the electronic ignition on the Main Power Distribution Bus (Z-14 terminology). Then when you turn on the master it will have power and if you turn on all of the crossfeed stuff it will have power from the secondary battery. Now the problem with this if something goes wrong with a unit on your Main Power Distribution Bus you can't power it down like you might want to without losing your electronic ignition.
I have a dual alternator single battery configuration, Z-13 effectively. I went with only a single battery since if it is maintained and replaced at regular intervals then I think I can minimize the risk of battery failure. Some may not agree but in other threads at least some agree. Now if you follow that same approach your primary battery is unlikely to fail and leaving the electronic ignition on the primary battery as I believe Bob was suggesting might be the best call.