The BiDi algorithm operates on paragraphs of texts.
In terminal emulators, the reasonable definition of paragraphs, hence the one we will go with, is the segments delimited by explicit newline characters (I’ll sometimes refer to these as hard newlines). A paragraph appears as one or more rows of the emulator.
In the unlikely case that an emulator doesn’t yet have this concept, it will have to introduce and track it for the sake of BiDi.
Most terminal emulators already track which of the lines were terminated by a hard newline and which by a character wrapping to the next line. They use this information e.g. for selecting text on double or triple mouse click, copying the selected text to the clipboard, or when autodetecting URLs. Emulators that rewrap their contents on resize also use this very same concept of paragraphs for this operation.
On the alternate screen, most apps (or libraries) produce output where each line ends in a hard newline, hence paragraphs become equivalent to lines. This is just a convention, not a technical necessity. Even on the normal screen, paragraphs typically consist of a few lines only.