Well there are a number of basic things like this that have no threads - I think most mods do not change everything (they are not full-conversions) and most of the full conversions never get that far because they are a serious investment of time and usually fold! ;)
Morale, of course, is not displayed but judging by the code it probably works in the same way as the exp - the unit recruited from a settlement with a morale bonus gains that morale bonus and it remains with it permanently.
To change the affect from settlement-wide to faction-wide you will need to use the faction capability code segment in the EDB file, tied to a unique resource/hidden resource in order not to duplicate the effect.
That will work if you allow for the effect to be won/lost but otherwise you will need to make it settlement-wide and place it at every level of the core building with the relevant faction as a requirement, which I assume is how Adherbal is implementing it.
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