For a while, it appeared that Dr. Vegapunk had a firm understanding of the science underlying the replication of Devil Fruit abilities. With the help of Momonosuke's Devil Fruit and the Seraphim powers that were duplicated, he had already demonstrated his success to some extent. Any Devil Fruit could now be produced artificially, which seemed to threaten the One Piece storyline. The procedure isn't as easy as one might believe, though.
In Chapter 1070, "The Strongest Form of Humanity," Vegapunk discussed his capacity to duplicate Devil Fruit powers. He can combine their skills to some extent, but it's a time-consuming and expensive process. As a result, there are a finite number of Devil Fruits that can be produced through science.
What Varieties of Devil Fruit are Artificially Reproducible?
The Zoan varieties of the three varieties of Devil Fruits in existence came the closest to being successfully reproduced. However, Vegapunk had to spend an excessive amount of time, money, and resources on it. Even then, he wasn't able to replicate Zoan Fruits perfectly, and he's not even sure if they can be Awakened. They can also be mass-produced as Caesar Clown's SMILEs, but those Fruits are morally dubious and aren't as good as the originals in general. While it is possible to duplicate these Fruits, doing so is very difficult.
Recreating Paramecia types has been met with limited success. The only way Vegapunk could give someone else the power was by taking the bloodline elements from a living user to create Green Blood and confer that to someone else; in Vegapunk's case, he gave Green Blood to the Seraphim. While this isn't a perfect recreation of these types of Devil Fruits, it's still a usable workaround.
Unfortunately for Vegapunk, Logia types are a bust. He tried everything he could think of to reproduce them, but nothing came of it. This is the only class of Devil Fruit that was completely beyond even his comprehension.
Giving the Pacifistas artificial means of mimicking the Logias' abilities is the best compromise he could come up with. A Pacifista could be filled with the desired element and used to blast it out because a Logia Devil Fruit is essentially just a device for controlling a single element. Using Admiral Kizaru's Glint-Glint Fruit and lasers, he has already accomplished this. Other Logias, such as the Plume-Plume Fruit, the Flame-Flame Fruit, the Rumble-Rumble Fruit, the Ice-Ice Fruit, and the Gas-Gas Fruit, should yield similar results for him. The Logias' intangibility may be lost to the Pacifistas, but they should still be able to use their elements.
That even Vegapunk has this much trouble creating fake Devil Fruits is probably for the best. If he didn't, the World Government might order him to raise a force of Pacifist Mag-Mag Fruits. Even Luffy and all of his allies would be helpless in the face of such a force. This restriction maintains the proper balance of power while still introducing a fresh, intriguing idea to the One Piece universe.