I have a hard time thinking that was planned. The gate is at the edge of the lagoon. And SSE is far away on the other side. So, it would be rather difficult to *not* get SSE to appear in the gate. You can get the Big Blue Box to be perfectly aligned with the gate. Or any other Future World building.
I have a hard time seeing it as anything but
very deliberately planned. I don't know that I've ever seen an authoritative quote referencing it (and I'd be glad to be pointed at one if there was), but the geometry of the site plan couldn't have been an accident:
First off, if you look at the orientation of the south World Showcase pavilions, the primary axis of the pavilions are deliberate. At first glance you might assume all the pavilions point to the center of the lagoon. Turns out, they aren't even close - the axis of the 3 center pavilions - Japan, USA, and Italy, orient their centers perfectly to the center of Spaceship Earth (red lines below). The flanking countries of France, Morocco, and Germany all converge not to SSE but to the primary WS overview point at Showcase Plaza (in blue)... the only place In EPCOT where you can literally see the whole world. (er, at least until these barges show up...)
Now that we've established a center line of the pavilion linked clearly to SSE in concert with the rest of the park's plan, we can look at the Japanese pavilion itself:
The Torii Gate perfectly splits that centerline, and also is perfectly rotated perpendicular to it. It is notably
not square to the WS promenade itself which jogs perfectly E/W on its run through Japan.
Yes, you can rotate your placement and field of view through the gate to put anything in the background including the Guardians building, but not if you stay perfectly on the centerline and render the gate symmetrical and balanced in your image. You do that, and there's only one thing you would ever have in the background (1983 image from Yesterland, modern view Google Streetview):
When I look at a picture like this, I tend to think that even the orientation and profile of the island was deliberately tweaked to 'make' this picture from Day 1, playing to that centerline and intentionally using nature to provide an asymmetrical element that juxtaposes the rigid symmetry of the gate / SSE composition. EPCOT was designed by filmmakers. It's a cinematic shot. Without the island and the trees, it wouldn't be as interesting of a picture (it actually looks better today, I think, with the fully grown pine trees).
Without a guiding hand in the overall site design, there's no way all of those elements would have lined up by accident.