Yeah, from the interview in the OP
English translation of the Kōzō Morishita 'GT Back Then' interview from the 2006 Dragon Ball GT Dragon Box DVD release in Japan
www.kanzenshuu.com
I mean, there's literally an entire episode worth of GT Vegeta reminiscing on his past and we get an entire highlight reel of Z Anime scenes that differ from how said scenes happened in the manga (episode 55), and the ending also has a highlight reel of the Z Anime.
Aside from that, GT Goku references the time he fell into Hell in the Saiyan Saga, which is explicitly an Anime filler original scene.
So I'm not sure how literally the "side story of canon DB" comment from Toriyama can be taken as meaning it's part of the manga timeline, though I suppose what the OP proposes about it being a different timeline makes it work.