Tom I'll be frank with you. you have the gamma, so you know more about its precise layout, however I've been here since beta 1 and have gotten
very cozy with the current system, so for all I know we may be talking on two completely seperate levels of two completely different menus.
however I would seriously disagree if you were to tell me that these features were ever impeded because the use is in another screen. I've seen battles where the bounty swells up into thousands of credits within the first 10 minutes, and hits tens of thousands by midgame! (admittedly we dont have the timer yet, so I havent experienced that sort of rush, but I look forward to it

)
black market is more or less an as-appropriate thing. if you are constantly selling and buying off you're making a bad investment as money goes into the nice sinkhole that is middleman transaction

. if someone makes their investment in an eclectic planet I still doubt the time they would spend inside the menu would exceed half a minute within the early game.
I have played rise of nations, and I would contend that the system is slightly less complex than Sins's, and that given the condition of Sins's current layout those buttons wouldnt be nearly as neat or discrete as in RoN.
finally, and i think this is the kicker: I tend to discretely segment my time, I rarely if ever go into blackmarket while I'm micro-intensively handling a battle or zoom in on a battle when I'm planning upgrades for my planets. going in and out of one menu is less disorienting to me than going between two consecutive planets.
I know it takes some getting used to, but its in my own personal opinion that taking something that has uses as eclectic the black market and bounty board and putting them where they would clog other functions, or worse, replace more important functions would be unhelpful and at the very least, mildly irritating.
(think of how much space the pirate bar would be! even baring the visuals and the timer it would have to accomodate 10 decently sized buttons with big, clear numbers that range into 5 digits!)
maybe its just a matter of preference, but this is my own personal belief on the issue. obviously its not optimal, but until we all have 30" computer monitors I dont think it can be handled
Edit: as for your modding concerns, I'm sure the interface will be adjustable.