So far I noticed it will only increase the base stats above all the affixes (that appear in white only). Whenever I do this I will get a slight increase in force shield/AR/health if the base is in white font.
If the item already has extra health/FS/AR as a magical affix (in blue) then I notice nothing changes, even if there is room for more stars to be filled in. And I have put in some items with only 3 affixes and it still did not come out with 4.
When I make a rare into a legendary then I will get more affixes, up to 6, if it had 4 to begin with.
I'm still testing this but before the patch if I upgrade a sub-5 star item to legendary then the base defense numbers did not change, so I figure for now if it's a good item I upgrade all the quality to 5* then increase rarity to legendary.