The first issue is inconsistency which I’m going to address early next month by having all the “views” processed through view templates (not just sales invoices).
I think the issue is that
Notes field on invoice is processed through Markdown. Markdown will wrap each line into a paragraph (that’s the reason for wide spacing between lines). You could possibly wrap the notes into
<p> tag and then use
<br> tags to break lines. This would override Markup default behavior.
<p>I'm a note<br />and this is second line<br />and this is third line</p>