It is possible to cut the render at the end of a specific line. That is, define a start line and an end line to render. This is feasible for the tools. Then, you must correctly synchronize the notes according to the duration of the lines.
Can’t you take the duration of the lines as a reference before rendering? Everything is much easier if you use the bar correctly, the rhythm.
You can try SamRender, to see if it fits your needs… At least you can load each render directly on a new instrument. And if necessary, edit there.