AT90USB is defined in pins.h

Marlin/Conditionals.h

 
   #define CONDITIONALS_H
 
+  #include "pins.h"
+
   #ifndef AT90USB
     #define HardwareSerial_h // trick to disable the standard HWserial
   #endif
     #include "WProgram.h"
   #endif
 
-  #include "pins.h"
-
   /**
    * ENDSTOPPULLUPS
    */

Marlin/Marlin.h

 
 #include "fastio.h"
 #include "Configuration.h"
+#include "pins.h"
 
 #ifndef SANITYCHECK_H
   #error Your Configuration.h and Configuration_adv.h files are outdated!