Not sure if you are aware, but the Saber class is basically the "Mario" of Fate series--meaning it has the most diverse skill list of all the other classes, being quite strong in almost every factor. Hence why it is viewed as the strongest class. Naturally it all comes down to its Master as well, and how great of a mage you are. But even there, there are aspects that can play into what makes the class strong in different areas.
Lancer was taking the best of Saber in the first round (and had he used "hit and run" tactics, they could have won the war), but the second time Saber was getting the better of him, due to her knowing his skills. Gilgamesh is a formidable foe for sure, but not unbeatable. Sure, Saber had no chance at that stage, mainly do to her being severely weakened after fighting Berserker. Rider is an interesting match, but it is hard to say how it would turn out where he to use his Noble Phantasm.
There are a lot of points that can be taken into consideration, and while there are certain rules and structure during the war, nothing is set in stone when it comes to fighting between the Servants.