spring-boot: spring.profiles.active in default properties ignored if defaultProperties contain a value for that key

As per documentation here a boot application is suppose to override properties that is defined in files in the given order.

So consider this situation.

I define spring.profiles.active and set it to dev using SpringApplication.setDefaultProperties which is last in the order. So that my application always has a profile by default.

Now I set spring.profiles.active to prod in my application.yml file and since its in a higher order I would expect this to override what I set earlier above.

But thats not happening, My application doesnt take prod profile and I see this debug log

com.mycompany.myapp.TestApp              : Starting TestApp on DESKTOP-3NUQHBI with PID 14436 (D:\Projects\test\testApp\target\classes started by Deepu in D:\Projects\test\testApp)
2016-05-20 17:07:48.045 DEBUG 14436 --- [  restartedMain] com.mycompany.myapp.TestApp              : Running with Spring Boot v1.3.5.RELEASE, Spring v4.2.6.RELEASE
2016-05-20 17:07:48.046  INFO 14436 --- [  restartedMain] com.mycompany.myapp.TestApp              : The following profiles are active: dev
2016-05-20 17:07:48.046 DEBUG 14436 --- [  restartedMain] o.s.boot.SpringApplication               : Loading source class com.mycompany.myapp.TestApp
2016-05-20 17:07:49.085 DEBUG 14436 --- [  restartedMain] o.s.b.c.c.ConfigFileApplicationListener  : Activated profiles dev
2016-05-20 17:07:49.100 DEBUG 14436 --- [  restartedMain] o.s.b.c.c.ConfigFileApplicationListener  : Profiles already activated, '[prod]' will not be applied
2016-05-20 17:07:49.100 DEBUG 14436 --- [  restartedMain] o.s.b.c.c.ConfigFileApplicationListener  : Loaded config file 'classpath:/config/application.yml'
2016-05-20 17:07:49.100 DEBUG 14436 --- [  restartedMain] o.s.b.c.c.ConfigFileApplicationListener  : Loaded config file 'classpath:/config/application-dev.yml'
2016-05-20 17:07:49.151 DEBUG 14436 --- [  restartedMain] o.s.b.c.c.ConfigFileApplicationListener  : Skipped (empty) config file 'classpath:/config/application-dev.yml' for profile dev
2016-05-20 17:07:49.152 DEBUG 14436 --- [  restartedMain] o.s.b.c.c.ConfigFileApplicationListener  : Skipped (empty) config file 'classpath:/config/application.yml' for profile dev

But if I set spring.profiles.active to prod in Command line arguments its working as expected.

I would assume that this is a bug as the behaviour is different from what is documented.