I haven't seen the boats in question, but one difference I have noticed on my own boat.
It came with Waylander Marine 25 gallon tanks, which were stock at around this time (early 2000's). These tanks were wide set, so there was a lot of space between them. On the other hand, they went right up to the bottom of the splashwell, and also "stuck out" forward of the splashwell lip (hence why those boats don't have the full coverage fuel tank covers that tuck under the splashwell, but instead have 3/4 height starboard partial covers).
I then bought the "current" 23-gallon Moeller tanks. These are set closer together (less space between the two), and there is a bit of room at the top (unless you have a newer boat with the cockpit sole molding, which is why they were cut down slightly). However they line up with the splashwell lip, thus full fiberglass covers fit (the ones that tuck under the splashwell lip). I like the tanks being flush with that lip, but they do give up some "in-between" space.
There were also, briefly, 25-gallon Moeller tanks, before the inch was taken off the height to accommodate the "permanent" cockpit sole and tank liner setup. Unfortunately Moeller cannot sell these as the owner of the rights (or whatever the correct terminology is) is some way-back, unknowable, previous C-Dory maker. The current 23-gallon tanks they do have the rights to make/sell.
Anyway, upshot is that the Waylander 25 gallon tanks (early 2000's) have more space between them (I can't remember exactly but maybe something on the order of 5-6" more).