Before Xiang Beifei entered the Heavenly Connection realm, when he met the Ghostly Visage with Ghost Whiskers and the Meat-Winged Monster, he did not see their Dao embryo. One reason was that Brain Deficient and Ye Ji were only in the late phase of orifice transforming, having not yet communicated with the Heavenly Dao, and another was that at the time, Xiang Beifei hadn't yet comprehended what Dao was.
As for why he initially saw the Human Race's systemic Dao embryos in Jiuzhou, it was because the Human Race's Dao embryos were relatively special, though it could also be due to modifications made by his grandfather—it was hard to say.
But now, he had acquired abilities akin to controlling a system.