The ER is planetwide yes, but the max number of buildings allowed before they become less effective thing (can't remember the acronym) is per city, so a city of just offices or something would be effective for generating jobs, but not income.
And yes you culd build a city full of jobs and then a city full of flats. SBR works off of civ level and stuff to figure out how many of each type you can have per planet.
If there is no populace facilities will lose money. Unless you meant there's a good ER but all flats are in one city and all jobs in another. In that case as long as you don't exceed SBR then yes they will make good money. Just imagine everyone takes their speeder for an hour to get to work :)