Generally your feet are spaced much wider on an mtb than on a road bike because of the triple chainset and wider tyres, meaning the frame is wider at the chain stays, and meaning that the crank arms need to be wider to clear them. You won't be able to replicate this width on your road bike, and your shouldn't try to as the theory goes that the narrower the width, the better.
In reality (and this is a bit difficult to measure), your feet should be spaced in a natural position. Stand up with your feet spaced in a naturally comfortable position. Measure the width between your feet and try to replicate this on the bike. The trouble is you probably won't be able to measure it to the nearest 2.5mm, and you probably won't be able to replicate it anyway. What is probably true is that the spacing on your MTB is too wide for your natural position and your road bike will enable you to get closer to it.
The 2.5mm spacing adjustment is there to offer you a bit more heal clearance if you ride 'heals in'. My advice would be to set your feet as inboard as possible, and if you clip your heals, move them out the 2.5mm (which is a tiny ammount in reality).
In terms of pedalling efficiency, you are spot on with the ball of the foot method for the cleat position. Any deviation from this might put pressure elsewhere on your foot and lead to hotspots and discomfort. If you follow my original advice about a bike fit, you might discover something different in terms of the relative length of your upper and lower legs, but for the moment, go under the ball of your foot.