I use TinyTex.
But actually I found why those characters weren't supported when knitting to PDF: it was because part of the text in the Rmd was pasted from another document and the character was oddly encoded.
For the second question here's what I have:
Anatomy <- read.delim("Anatomy.csv", sep=',',dec=".",stringsAsFactors = F) %>%
kable(Anatomy[1:6,],
format = "pandoc", escape = F,
caption = "Table de données de la description anatomique (exemple des lignes 1 à 6)") %>%
kable_styling(bootstrap_options = c("striped", "hover"),font_size = 7)
What gives a cropped table once knitted:
