There's several reasons why this could be, here's a few that...
1) Poor quality control. Some planes look good, but have imperfections that cause balance issues, trim issues, or even problems with the electronics.
2) Cheap crap. Sometimes there's a really good RTF airframe that is only available as a RTF or "Ready To Fly". It's sold at a really low price, so the electronics inside it are the cheapest available. It might be worth it to a pilot to buy the RTF version, gut it, then replace everything with higher quality components.
3) Personal preference. Some people just like to fiddle with things. They want more power, they want different flight characteristics, they want their plane to look different than everyone else's.
4) Availability of on hand supplies (consumer). In some cases, you might have a plane that calls for a certain sized battery, but you don't have it. So you can combine two battery packs, to do the same thing, either more voltage, or more mAh.
5) Availability of on hand supplies (manufacturer). Sometimes the manufacturer puts together a plane package, that when designed, intended to use a certain motor and battery combination, but when it was produced, and was ready for market, went with a different combination due to availability, or cost. The change in motor or available battery, might have ended up being heavier, or lighter than it was originally designed for.
6) Lost in translation. Much of what we're flying is made in China. Keeping costs down, lots of corners are cut. One of these corners seems to be the quality of the directions, and to compound that, the quality of the translation of these directions.
There's a few things that come to mind. Hope this helps.