Hi,
Theoretically no, but practically yes.
Your entire website width size is constant 960px now, if you enlarge or decrease this width size through joomla template configuration (I am not sure if your template lets you change it and Why you would do that by the way!!...).. then you will end up with misalignment problem again, then you should alter this fixed 303.333px value to which ever is the best for you.
Probably something was limiting the width size to a smaller value, this is why the 33.33% didn't work out for you at first. Using percentage for template developers is good because this would work all different situations no matter what the entire width size of the website is. But having fix values like (303.333px) would work only in your specific website and you got this pixel value by trying, right?. But, yes, it is a right way. The hardest but still the "right"..
Regards.