The "equal runoff" may be the "ideal" but even if they're unequal, it's not going to make all that huge a difference. You might get slightly lower efficiency but, as long as you're consistent, you can account for whatever efficiency you regularly achieve.
That said, if 3.5 gallons is all you can get in your cooler with 12 pounds of grain, that comes out to 1.167 quarts/pound. That puts you at the lower end of the range (thicker mash) of the normal 1 - 2 quarts/pound. Since at least 1.25 and probably, even better, 1.5 quarts/pound is an "ideal" ratio, you might seriously consider a new cooler. Get a cheap rectangular 36 to 48 quart (or even maybe larger) cooler and use Denny's "braid system" and you can have a brand new mashtun for very little money.