Lacking Kishi's involvement and being canon are different things entirely. Specially when Kodachi is involved, who is main writer of Boruto and comes up with all stories and plot-lines on his own, meanwhile Kishimoto remains separate for most parts.
Not being written by Kishi and never been labeled as canon by Kishi is really all that needs to be said.
Yes, if there are any inconsistencies, ofc Manga is given precedent. She doesn't need to say that for anyone with common sense to understand. It being "only truth" encompasses Boruto, as well, btw, Jun is essentially saying Kishi's work takes precedent over every single material outside of Naruto manga.
"It's sure that the original comic is one and only truth"
The author is outright stating that the spin-offs aren't the "truth", they aren't canon. They're a way to enjoy Naruto. There's no word of contradictions here, no word of errors. It's about the overall story itself.