Via asmock’s installation wiki, I stumbled upon a second way to link a custom FlexUnit4 runner into a Flash Builder 4 project: using a compiler argument.
Add the following to the “Additional compiler arguments” under “Flex Compiler” in your project properties:
-includes asmock.integration.flexunit.ASMockClassRunner
This way is probaby more straightforward than using a custom FlexUnitApplication, at least as long as you’re doing something simple.