Space after every five rows in kable output (with booktabs option) in R Markdown document

The reason why the row height is not always equal is that by default, kable inserts a \addlinespace every 5 rows when booktabs is specified as TRUE, as is shown here:

linesep = if (booktabs) c('', '', '', '', '\\addlinespace') else '\\hline'

To alter this, add linesep = "" as an argument to kable().

knitr::kable(
  head(iris, 20), caption = 'Here is a nice table!',
  booktabs = TRUE,
  linesep = ""
)

See Get rid of \addlinespace in kable for more details.

It is also worth saying that you can play around with this option if you want to change the style. For example linesep = c("", "", "", "\\hline") would add a horizontal line every four spaces.