When I design a ship, I make a decision between merchant and naval, with merchant bridges actually being bigger and more comfortable, since they usually combine jobs like communications and sensors, while a naval vessel will have these seperated and often doubled seperately somewhere else, just in case.
As for the problem with the bridge size, I usually rebate a sickbay space and 1 airlock out of the bridge space, along with 1/4-1/2 of the computer and avionics, although never more than that and never more than a total of 10 tons on ships under 1000dt. Of course, I also charge 1/2 the cost for the sickbay, since the space cost has already been paid for.
I cheat a little in figuring out where I get space for corridors and the like, without shorting passenger cabins and the like. Headroom is given as 3 meters but I give it 2.2 meters for headroom, .3 meters for ducting, cabling and the like with a secondary ceiling and use the extra space 1.5 x 1.5 x.5 meters for corridors and public areas. The only areas where I do not 'steal' this space from is fuel storage and cargo space, since these are fully used to begin with.