Heat oven to 350°F. Cut a shallow lid from the upper third of each croissant and gently remove enough soft crumb from the bottoms to create four pockets about 1/2 cup each, leaving the bases and walls intact; reserve the removed crumb for another use.
Mix pork, sage, fennel, salt and pepper. Heat oil in a skillet over medium heat and cook the pork for 6 to 8 minutes, breaking it into fine crumbles, until browned and 160°F; drain and cool for 5 minutes.
Whisk eggs with milk and scallions. Arrange croissant bottoms snugly in a baking dish, divide sausage and 2 ounces Pepper Jack between the pockets, then slowly divide the egg mixture over the filling.
Scatter the remaining ounce of cheese over the pockets. Cover loosely with foil and bake for 18 minutes, then uncover and bake for 7 to 10 minutes more until the centers reach 160°F and no liquid egg remains.
Warm the croissant lids on a separate sheet in the oven for the final 4 minutes. Remove the boats and rest for 5 minutes so the egg filling settles.
Set a warm lid on each filled bottom and serve with a knife and fork or let cool briefly enough to hold.