Okay, here's a quick - and almost certainly inaccurate - example of what I think the Imagineer was saying.
If you measure the halfway point between the entrances to The Land and Mission: Space, it's slightly to the east of EPCOT's centerline. (Remember, "up" is south in EPCOT's orientation, and "down" is north.)
Likewise, if you measure the halfway point between the entrance to France and the Africa expansion pad, it's slightly more to the east of EPCOT's center line.
Here's a badly-drawn illustration of that:
View attachment 672646
Of course, Harmonious' alignment is more skewed than that. But the thing is, the points you pick for the east and west boundaries in Future World and World Showcase can result in a park centerline that's not aligned with SSE and the American Adventure.
Why would anyone do this?
The only thing I can think of is that if the World Festival pavilion was built, the prime viewing spots there would have a centerline slightly to the east of the SSE-American Adventure centerline. That festival sightly line would be perfectly aligned with the sight line that got built for Harmonious' barges. I leave it to someone else to draw that line on a map.
So my guess is that they aligned Harmonious' barges off the centerline, in the expectation that the show would last for 10-20 years and the World Festival pavilion would be built by now, generating lots and lots of dessert party revenue.