Confirmed as spring boot bug in https://github.com/spring-projects/spring-boot/issues/44849

Sadly, no fix can applied to all classes, but to minimize the changes, we can either:

a. Use @Autowired to make constructor not used for property binding:

class CustomA @Autowired constructor(
    var y: String = "",
    var z: String = "",
) : Base()

b. Declare subclass with only default constructor

class CustomA : Base() {
    var y: String = ""
    var z: String = ""
}