TypeScript's “Combine JavaScript output into file” option doesn't infer correct script order without /// <reference> tags

I'm working on a TypeScript solution that uses the "Combine JavaScript output into file" option:

I'll often reference an item defined in another file, for example:

In MyBaseClass.ts:

export class MyBaseClass { }

In MySubClass.ts:

export class MySubClass extends MyBaseClass { }

While developing, Visual Studio has no problem understanding that MySubClass references the MyBaseClass defined in MyBaseClass.ts - the solution successfully builds and I can navigate to MyBaseClass using F12.

However, I run into runtime errors when I run the solution because the generated JavaScript file defines MySubClass before MyBaseClass.

I can fix these runtime errors by adding a /// <reference> tag in MySubClass.ts:

/// <reference path="MyBaseClass.ts" />
export class MySubClass extends MyBaseClass { }

Why does the IDE understand the relationship between MySubClass and MyBaseClass, but the compiler doesn't correctly order the definitions of these classes in the generated output?

I'd either like the generated output to correctly infer the order of the class definitions (preferred) or the TypeScript compiler to throw errors if the /// <reference> tags aren't present.