I find these types of marker rather unimaginative as control indicators.
My version of Conquest of the Empire combines control markers with “Governors”; i.e. instead of placing a generic faction marker you place a piece of your player colour with a name and portrait of an official representing the new governor of that province, who might have variable stats e.g. +1 combat/die re-rolls to be applied when fighting in defence of that province.
A similar system could be used in modern era games with the governor replaced by a “General” who is considered in command of friendly forces in the tt. This character can take command of forces moving from that area into hostile tt, and if successful a new commander is taken to replace him. Generals captured in battle might score victory points. Naval commanders can be used to be placed in control of fleets “at sea”, though I don’t believe ships should ever be considered at sea between turns.
Conversely, I’d move towards always having to have an infantry unit present to continue control of occupied tt. If you abandon an occupied area a native general/infantry unit is generated to take back control.