Try setting the jasmine.DEFAULT_TIMEOUT_INTERVAL in a beforeAll, since the timeout interval is reset for each it block:

describe("testing timeout", function() {
    beforeAll(function() {
        jasmine.DEFAULT_TIMEOUT_INTERVAL = 999999;
    });

    fit('should have custom timeout', function(){
        console.log(jasmine.DEFAULT_TIMEOUT_INTERVAL); //prints 999999
    });
})