But the combat script has no way of detecting if Hero has Logistics. The override patch RTA and other PvP mods use breaks the 5.5 framework. On the side note, I am interested why do you think starting ATB bonus is reasonable or more meaningful than bonus creature giveaway? or it is just a personal preference towards a more combat-involved effects?

It is preference towards unique, clear 100% combat-involved effect which is in demand.
You have Sorcery + Swift Mind - for hero initiative (starting ATB + later initiative bonus).
But you have only Leadership - for units initiative (only later initiative bonus, without starting ATB).

When do you want to have ATB-based Logistics? Everytime you want to move earlier than opponent in the battle.
When do you want to have creature-based Logistics? Everytime earlier game, no matter what is needed in the battle itself.