Overriding flags in qmake.conf

How do you override the values of qmake.conf?

For example, I wanted to add -msse to my project.pro file, so I entered the following:
QMAKE_CXXFLAGS += -msse

That works. But I also wanted to compile for the native architecture, so I entered the following:
QMAKE_CXXFLAGS += -march=native

When I qmake, I see that -march option appears twice! It appears first with the value defined by qmake.conf and then is followed by the option with my value. I am guessing the second one overrides the first, but I'd like to know for sure.

What's the point of modifying qmake.conf? Can't you put those statements in your project file?