Pagination in pdf output can be difficult, especially with long tables (figure placement is, too).
While there are various packages, such as {kableExtra} to give finer control over table layout even if they do wrap the columns, there is no guarantee that the table won't still overflow.
Rmarkdown produces an intermediate tex file used in the auxilliary program pandoc to convert the output into the \LaTeX markup language from which the pdf is generated. It's possible to edit that file to further control the display, using macros such as its longtable package. Learning $LaTeX$ requires a substantial investment in time, which is not for everyone.
One approach, which probably not be suitable for publication quality, is to chop the table into multiple data frames.