There’s a much simpler, and more-widely-applicable, answer: it’s to make the bottles stand up straight without wobbling.
A little thought will make it obvious that in order to stand steady on a flat surface, a bottle has to have a flat bottom; if it doesn’t, you get that problem that bedevils amateur table-makers: the legs don’t all touch the floor, and the thing wobbles, often giving comedy. One solution is to make the bottle so that only a circle on the outside of the bottom is flat, and all of the rest of the bottom is raised above that ring. Nearly all bottles and jars out there today, no matter what they contain (from mouthwash to mayonnaise), adhere to this basic design.
This problem is magnified when you’re making the bottle by hand, which involves a device called a punti (there are many different forms of the word). This is used to hold the bottle so that its neck may be formed and then completed. The problem is that a punti leaves a mark on the bottom of the bottle: a “punti scar” which may be small or large. In order to keep the punti scar from making the bottom of the bottle uneven, the glassblower pushes in the bottom while the glass is still soft, which leaves the punti scar raised above the ring at the outside of the bottom, and thus safely off the table. The indentation left in the bottom of the bottle is even called a “punt” in obvious homage to the punti scar.
As Cecil noted, unscrupulous sellers of high-priced commodities like wine and champagne realized that the indentation reduced the capacity of the bottle, while leaving the bottle apparently full-sized, thus simultaneously short-changing the buyer and hiding the fact from all but the careful. If a small punt was good for business, a larger one must be better, and you find some bottles with remarkably large punts in them.