For FTIS, the FAA did not mandate a retrofit, only a forward fit.
IIRC authorities only require that tank "flammability" remain under a certain level. (definition of "Flammability" is provided)
FTIS is just one solution among others, although it is of course the most obvious one.
When fuel tank inerting systems were first discussed as an important safety system it was often acknowledged that any major change like this could have the unintended consequence of being a possible hazard in certain situations.
Indeed, adding systems on top of a basic design, even if it is for safety purposes, will complexify the initial system. Which increases the chance of something going wrong. The book "Normal Accidents" even concludes that at some point the whole thing becomes so complex that accidents are unavoidable (IOW are the "norm" for such systems). Debatable, but the basic idea is sound.
In this case however the FTIS is the solution, not the problem. Through various interactions with other systems, switching the FTIS to NO GO has impacts by ripple effect on the dispatch conditions of those other components. But this is only an operational headache, not a safety breach.