This feature of css-grid-3 allows developers to align tracks individually. However this creates a disconnect pretty quickly with the "visual order" and the "box order" of the document.

Example 9 in the spec demonstrates this well:
https://drafts.csswg.org/css-grid-3/#masonry-axis-alignment

The tab order for above would be 1,2,3,4... etc. However the visual order for that example definitely not that :).

The use-cases I've seen here typically align masonry axis tracks together rather than individually.

Something to lean on here might be something similar to how flexbox works in that you can start the masonry algorithm for the "end" side, instead of the "start" (e.g. row-reverse and friends).

Note this problem is different to alignment on individual grid/flex items, as for those layout modes alignment happens within a line/track, and the visual order still matches the box order.