How do bakeries get smooth jam to top their cheesecakes with?
You are thinking of jelly like actual jelly in a can: Sweetened fruit juice thickened with pectin. While some bakeries use special pectin to make glazes (look at LM pectins) most jelly fillings and glazes are made with starch. In the US, usually corn starch. 

Jelly donut filling is like canned pie filling: a sugar syrup that is thickened with starch. This is an example recipe.

Fruit glaze toppings are similar but have a bit more starch so they set up more firm. Here is a commercial example. Notice the ingredients, corn syrup and corn starch are prominent.



Starch is cheap, sets up firm and is less sweet than sugar. Pectin has a better texture and flavor, in my opinion. When making glazes at home, boiling down jams and jellies produces superior results.