There is a precident for "just ignore all the specified behaviours and do their own thing".
Moodle 'Essay' questions, irrespective of what the quiz 'How questions behave' option is set to, use the 'Manually graded' behaviour.
So, it is certainly technically possible to have it so that CodeRunner questions always use qbehaviour_adaptive_adapted_for_coderunner, ignoring the quiz setting. I can see arguments for that approach. For the student, writing code where you cannot run it, see if it works, and then fix it if necessary, is a completely inauthentic experience. Being able to vary the penalty strikes me as sufficient control for the teacher. Always using Adaptive mode strikes me as better then allowing teachers to select a different behaviour, then displaying a message on screen that it does not work properly.
As Richard says, the other way to go would be to make CodeRunner work with all Moodle behaviours, but this would be more work. It would be a lot of work to make ..._adapted_for_coderunner versions of all the existing behaviours. The other approach would be to make changes in Moodle core, so that the the set_qt_var bit is no longer needed. This is a long-standing request. See https://tracker.moodle.org/browse/MDL-30442. I quite like Richard's propsed way to handle this, which is backwards compatible for existing question types. That would only leave
adaptive_adapted_for_coderunner doing the enhanced penalty regime, which woudl be less code, and that bit would not be necessary for other behviours. (Of course, any Moodle core change could only go into Moodle 3.3, which would be released next May, so this is a long-term view.)
(While I am talking about Moodle core issues, https://tracker.moodle.org/browse/MDL-54959 looks like it also have the potential to simplify adaptive_adapted_for_coderunner if it ever gets done.)