Hi Juhan,
You're correct: the JavaScript embedding API is done specifically for forms created with Form Builder, and there is no JavaScript API for embedding forms created with plain XForms.
The API is for Form Runner mostly because it takes an app name, form name, mode, document id, which are all Form Runner specific, and uses those to build a URL. Creating a version of the API that allows you to provide any URL, wouldn't necessarily be a lot of work, but it isn't something for which there is a lot of demand at this point.
Do you have another way of handling this, or are maybe thinking of moving the forms to being created with Form Builder?
-Alex