I know this is the case for wine. Up to a magnum, the price is usually the same per ounce. However, once you hit 3L+, the glass becomes incredibly expensive - at my winery, they said it was due to the glass being hand-blown at that size (may or may not be true).This is not to be contrarian or justify anything about the pricing per se, but apparently larger format (1.5L and up) glass is much more expensive. I know that sounds crazy, but I have inquired with my local homebrew shop after reading on here and apparently the larger glass can run a pretty penny.
May not cover the who price delta, but it is a factor is all.