Your Makefile runs compiler with an option -mmcu=YOURCHIP. This implicitly defines macro corresponding to your chip. For instance for atmega32u4 the macro is AVR_ATmega32U4. Intellisense is run 'outside' of your compiler so it's not aware of this macro and when parsing standard avr header - like avr/io.h
it skips the proper inclusion of header file for your particular MCU. It's something like:
#elif defined (__AVR_ATmega32U4__)
# include <avr/iom32u4.h>
So, if you want to have intellisense support for stuff defined in those headers you might need to define that macro, at the top of your source, like this:
#define __AVR_ATmega32U4__
#include <avr/io.h>
int main() {
char a = PORTB;
}
You may find what macro corresponds to which MCU in the middle of this page