I vote for the inboard section of the flaps because there is more area there.
I surely hope we are talking about inboard/outboard as "distance from the fuselage" instead of the left wing vs the right wing! If it was me, if I had somehow convinced myself to do it partially, I would do the outboard (near the tips rather than near the root), because that has more effect on roll.
This is not about making the flaps or elevator more effective (although it does do that, too) but to reduce the variability of the leaks over the travel, which tends to roll the airplane in ways that you cannot otherwise correct.
There is no gap small enough to not benefit, unless it touches all the time, and there is no gap too small to make it impossible to do without binding up. The smaller gaps does make it more difficult, but I have built gaps that I carefully sanded and measured to be about .010", then sealed them with good effects and no binding. And unless you are doing extensive wind tunnel tests to configure it properly, leaving large gaps *doesn't act like a slotted flap* and doesn't make it more effective, quite the opposite. Leaving a large gap reduced the effect of the control surface - although a 3/32" gap with a .010 variation over the travel does have less differential roll effect than a .011 gap with a .010 variation.
I would also note that those who don't think any of this matters typically end up with much larger flaps.
Brett