The realms were governed by the rules of Heaven and Earth. The ability to fly was restricted to different cultivation realms in each level but also there was a maximum height no matter how much Qi they had at their disposal.
It was caused by density of Qi, Laws, and comprehension limits of each realm.
The Wings of Freedom was able to let the crew violate those rules of flight for the simple reason that its creator was a Sliver Tier Immortal. Just like his Nautilus Class vessels exceeded the ability over time due to his ever increasing expertise.
At such a grade, carrying a crew was easy, but Lind was nowhere close to a Shard Tier. He had also never had the chance to test if the lower quality ships could work at higher realms as they did not survive his ascension.
