The main difference between Boston cream and Bavarian cream donuts is that Bavarian cream has additional whipped cream added. Boston cream donuts are typically topped with a chocolate glaze, and Bavarian cream donuts are typically topped with confectioner's sugar.
Both creams are derived from a thick vanilla custard, though the Bavarian style is lighter because of the extra whipped cream. Because the difference in the filling is slight, many bakeries use the two names interchangeably to describe the filling. The traditional donut toppings are the key difference between the confectioneries, as chocolate glaze is used to imitate the glaze used on a Boston cream pie for Boston cream donuts.