You should look up what game engines the games use and read up on what they offer for input.
My guess would be that the game engine comes with the standard control scheme and if something works then why spend any money or resources on changing it? Indy developers are on a super small budget so even something that simple would eat into their earnings.
It's super simple to code but you would still have to code it, make a menu for it, new graphics blah blah, if the indy dev doesn't care about it for themselves they won't implement it.
Unless you're dealing with a heavily specialized game engine such as RPG Maker, I can't imagine that there's
any set of default inputs. When you develop a game, you'll typically use a prototype methodology where things are built up gradually. In the beginning, it's likely that you'll use hardcoded definitions to simplify the initial development process. In some cases, you may be trying to find out if your game idea is even worth it in the first place, and spending a while making customizable button mapping just isn't worth it for that sort of endeavor. In the end, you may have made a mistake like not making those hardcoded mappings easy to change (e.g. hardcoding the button in every location vs. a constant definition that is referenced).
Also, you may just not have the time to implement configurable controls. Creating the menu is only part of the problem -- and still a decent portion of it -- as you also need to setup how the information will be stored, how it will be read, and finally, once it's done, you need to test it out to ensure there aren't failures. That might not seem too bad, but you'll need to be able to test not only buttons but button combinations, and even different keyboard layouts (including those from different locales/languages).
The development time aspect is also why some games take the "lazy approach" and put some menus in a launcher that shows up before the game starts. It's simply far easier to add PC-specific options to an easy-to-create windows program than it is to build entirely new menus. Plenty of languages allow for WYSIWYG editing of GUIs and combined with the lack of a need for custom assets, it makes the whole thing much faster. The back-end ends up being the same as it still needs to read and modify the same files as it would if it was integrated.
I don't blame someone for disliking the lack of configurable controls. Honestly, I can't bring myself to play Kingdom Hearts because I keep trying to press 'X' to jump, and I just wish that I could remap the buttons!
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