I recently wrote up a manuscript (materials available to review) and found an issue with using longtable with papaja when trying to have a single-spaced table, although I think the issue is primarily when that table is presented with another short table. I had to wrap my longtable code with the following to make it work:
\begin{singlespace}
\end{singlespace}
I created a sample Rmd and PDF file to demonstrate the issue. You can download them via my Dropbox: https://www.dropbox.com/sh/hkd6t0qnhot3efx/AAB3Y7GeeO_ZczybQX6-XcQja?dl=0
As you have found you can adjust the line height of environments by means of header includes. All you need to do is to add a line that adjusts the line height for the longtable environment. So you're header includes could look as follows:
header-includes:
- \usepackage{setspace}
- \AtBeginEnvironment{tabular}{\singlespacing}
- \AtBeginEnvironment{lltable}{\singlespacing}
- \AtBeginEnvironment{longtable}{\singlespacing}
- \AtBeginEnvironment{tablenotes}{\doublespacing}
- \captionsetup[table]{font={stretch=1.5}}
- \captionsetup[figure]{font={stretch=1.5}}