We have plans to give more control over the appearance of the text styles, including line heights. But I wanted to point out that the line height in Agenda is quite normal. It is almost identical to that used in Bear (see screenshot).
Where people probably think it is bigger is that the paragraph spacing in Agenda is bigger. In Bear and other apps, there is no paragraph spacing at all, just the normal line spacing, and you actually have to type two enters to get a new paragraph. That comes from the fact that they are markdown editors, where double enter is a new paragraph.
Agenda uses standard styled text conventions, such as in Pages. You use a single enter for a new paragraph. To make a list, you use a list style, etc. If you stick to these basic conventions, you documents look fantastic. So much better than double spaced markdown IMO