Yes, you probably need to constrain those changes further, and I’d suggest:
at RUT in "\\io1 .+\\ior": "ɓay vəra’ vay" > "ɓay vəra’\u2028vay"
at JON in "\\io1 .+\\ior": "ɓay raw Zonas" > "ɓay raw\u2028Zonas"
This says, only at / in the book of Ruth (or Jonah) look within the context of \io1 ... \ior
for the matching text and insert the line break.
If you had lots of these, it might be easier to have a more generic rule like:
at RUT in "\\io1 .+\\ior": "(ɓay vəra’) (vay)" > "\1\u2028\2"
so that you only have one side of the change rule to think about (copy and paste the snippet from the text, and then add the parentheses to show where to make the break). The right hand side (replace with) would always stay the same.