@kanedo if I copy and paste this markup into a Manuscripts equation, I see the equation gets typeset fine, but the per-line numbering is not applied. Is this what you are seeing as well?
As a workaround, you could always include the numbering in a static form as part of the equation lines. I think a better longer term option would be for us to offer a styling option for equations to let you choose whether each line gets numbered in case of multiline equations.
This limitation of only numbering the entire equation, not each line / statement in it, is a result caused by the particular configuration in which Manuscripts renders LaTeX math with the MathJax math typesetting system: the math is rendered for various technical reasons in isolation from the rest of the document and actually the cross-referencing number we show on the side is presented "separately" from the equation. This brings big advantages (such as very fast loading of documents with embedded math markup), and the ability to present the document without even having MathJax available (something which we'll be using very soon when we release the first batch of web based collaborative features to Manuscripts), but also carries this downside. We certainly can work around it and add this styling option though, I've made a note of it as a feature request. Thanks!
CEO & Co-founder of Manuscripts.app Ltd