Just wondering out loud: In the early days of OpenType, was it ever suggested to register a feature (or pair of features) for Devanagari or other Indic scripts to select between stacking vs. side-by-side conjunct forms? (Analogous to features for, e.g., lining vs. old style figures.) If not, why not?
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The latter is the trickiest problem, because the Unicode control character model strongly presumes that traditional ligature forms are the default if they are present in a font, i.e. the formatting control characters can be used to prevent ligature formation in various ways, but there is no control character method to force ligatures if some other shaping were default. One can imagine glyph level ligature formation such that e.g. horizontal half-form or explicit halant could be the default, and then traditional vertical stacks could be handled in e.g. dlig, but for the reph and ikar reordering issue, since dlig and all similar discretionary features are applied after reordering.
This is what prompted me to suggest, a while ago, the idea of adding a pre-reordering discretionary conjunct alternates feature.
It just came to mind while I was reading a proposal for Tulu-Tigalari, and stacked vs. side-by-side is relevant but left as a font-level issue. I don't think it has any of the issues you raised.