The wheel sharing is a good point especially as you'd already considered it for the front hub dynamo. I'd only go for it if the transfer was minimal effort, ie same dropouts/rohloff axle plate, etc, but definitely a possibility. I was giving the overall design concept some thought last night and, for this type of bike, I keep returning to the idea of ensuring versatility. For example making sure the frame can take a rohloff doesn't meant you have to run one it just gives that bit of future proofing. Some ideas:-
OTP - if you're going for a complete bike then it's really just a case of shopping around, testing and settling for the closest match. A hub gear can always be run with a tensioner, it's hardly the end of the world.
Custom - I'd be tempted to try and cover as many bases as possible without compromising primary function, so I'd go:-
1. get a frame that can accomodate a wide variety of uses and kit:-
tensioning - I prefer dropout adjustment over EBB but either serves, previous negatives re dropout tensioning around rack/guard mounting and interference are resolved by the swing style dropouts, as well as the Paragon ones I use there are options from Salsa, Black Cat and others. but if you went EBB then I'd want a rohloff compatible left dropout and derailleur hanger on right
brakes - disc brakes all the way, I wouldn't even bother with rim brake capacity
brazeons - get them to bung on routing for rohloff cables and derailleurs and disc brakes, I prefer cable tie guides to the tubular ones, easier to put stuff on and off. 3 lots of bottle cages bosses, rack and guard mounts and anything else you may desire
tyre clearances - go big, why not, you can always run smaller when you want
geometry - I'd follow Thorns lead and, for a flat bar design, make the ETT longer, you could also design in allowance for a variety of forks. Say you had the basic design at 72/72 with a 390mm AtoC fork, 45mm offset which has clearances for 700x40 tyres with guards and a BB drop of 75mm, this gives a trail number in the mid 60s. You could bung some roadier style forks in there with an AtoC of 370mm, same offset, which would change the geo to 73/73, BB drop to 83mm and trail to high 50s, still allowing for about a 700x32 tyre. Or you could go the other way and use some forks around 410mm which would give you a BB drop around 67mm, 29er tyre clearances and angles at 71/71. So in one frame you can range from fast audax, through light tourer to offroad/roughstuff tourer, just by swapping the forks. But this is only possible if you design in the capacity to the frame, ie clearances, angles and the necessary strength. I know this as it's exactly how I designed my rohloff commuter/tourer, it's basically a 29er back end with a much longer headtube. The first incarnation was a full 29er, ie short headtube, but this meant skinny tyres in 470mm AtoC rigid 29er forks and it just looked wrong and mudguards were very hard to fit.
2. once you have a core frame, the above is achievable for anything from £700 to £1800 in steel or £1200 to £lots in Ti, then you can build up as you see fit. Having Rohloff capacity doesn't mean you have to use it. For commuting only I'd be tempted to bung in either an Alfine 8 or a 1x8 derailleur. When I did my lengthy commute my I-9 hub gear had the range 35.4 to 120.6 gear inches...I didn't really understand gearing when I chose the ratios. I never used gears 8 and 9, both over 100 inches, and after I got fitter never dropped below 3rd gear at 47.5 inches. So nearly all of my riding was from 50 to 90 gear inches.
3. tempting as it is to start out with a complete bike with all the bells and whistles by getting the core frame versatility you can then go in stages. Prioritise the functionality via a cheaper gearing setup and spending more dosh on a quality dynamo setup. Then if the fancy takes you a future upgrade to fancier gearing whether rohloff, alfine 11 or derailleurs is always on the cards.

Just some more thoughts from the madhouse to confuse you