This appears to be out of your control.

Quicktime Components register various bits of information about the formats they support. A QT application then specifies what its requirements are and QT tries to find the component which best matches the requirements.

However, where multiple components support the same format/codec, I can't find documentation on how QT decides which component is "best."

See, the Apple docs just aren't particularly enlightening:

"The OpenADefaultComponent function searches for available components and attempts to open a connection to a component with the specified type and subtype. If more than one component of the specified type and subtype is available, OpenADefaultComponent selects the first one in the list. If successful, it passes back a component instance that identifies your connection to the component."

The docs don't indicate what controls the order of the components in that list. A QT application could certainly be written to provide the user a choice when multiple codecs are available, but QT player does not.

The most likely answer is alphabetical. Maybe you could put certain codecs higher on the list by changing their name so they come first alphabetically?