One of the problems in this context is the phrase "original meaning". What
we have is a juxtaposition of two words, which is indicated by writing the
letters of one with the vowels of the other. In many cases this does not
cause much of a problem, because the vowels fit the letters, but sometimes
they do not. Except for the most frequent cases, there normally is a note in
the margin with the alternate letters - I hope everyone agrees that notes in
the margin are not plain text.
Are you making here a parallel with the annotations added on top or below ideographs in Asian texts, using the ruby notation (for example in HTML) which may also be represented in plain-text Unicode with the interlinear annotation?
Are you arguing that interlinear annotations are not plain-text? If so why were they introduced in Unicode?
The notations in questions are not merely presentation features, they have their own semantic which merit being treated as plain-text, because their structure also ressembles a linguistic grammar, not far from the other common annotations also found in Latin text with phrases between parentheses or em-dashes.
Plain text is widely used since ever to embed several linguistic levels, which are also often represented too in the spoken language, by variation of tonality. The content of these annotations is also plain text. The graphic representation itself is not that important, it is just there to easily demonstrate the relations that exist between one level of the written language and the annotation language level.
If a text appears to mix these levels, there's no reason not to represent it. These annotations are present in the text, there must be a way to represent them in its encoding, even if it implies encoding mixed words belonging to different interpretation levels (such as Qere and Ketiv texts in Biblic Hebrew).
You are arguing against millenia of written language practices, just too much focused on the common Latin usage where many concessions to your intuitive model have already been integrated into Unicode (think about the various characters that have been added as symbols or special punctuations, or about other annotations added on top of Latin letters such as mathematical arrows...
I see less problems with the correct representation of Ketiv and Qere annotations mixed within plain text, and rendered as supplementary letters on top or around the core Hebrew letters, than with the representation concessed to the Latin script for various usages (including technical annotations or punctuations, or formatting controls...)
