I'm not knowledge w.r.t Japanese typography, but I assume IVS means Ideographic Variation Sequence here?

Yes.

I tried official release binaries in order.
Version 0.11.1 works as my expect.
The problem appears from version 0.12.0 Candidate 1.

Looks like line breaking strips out trailing default-ignorable characters, which include the variation selectors, from each line. I think we need to reconsider what characters can be safely stripped from the end of a line.

Another option is to perform trimming when collecting the elements; I have a proof of concept on my fork of the repo, but it results in some subtle changes in output right now.

We should probably investigate what other engines do...

I checked what SILE did and I couldn’t find anything related to special handling of default ignorables. I think SILE just uses what ICU4C does.

I think the test failures on my mf/collect-side-trimming branch are from differences in when an empty Text item is emitted. I don’t know how that could affect layout, though.