When I attempt to render a markdown document to pdf (using either pdf_document, or pdf_document2 from bookdown) I cannot get the included flextable (adapted from document I am referencing) to display as desired. This has been particularly frustrating as in Rstudio visual markdown editor the table displays as desired. I have attempted to use autofit() and set_table_properties(layout="autofit") to no no avail. Using the markdown script below I get tables that look like 
and
when my desired output which is how it appears in visual editor is 
I thought it could be due to complications with the merging of cells, borders and the theme, but even when I strip it down to a bare flextable I run into the same fitting issues. Rendering to html everything looks fine. All the posts and documentation I have found indicate it should work as written, not sure what I am missing.
---
title: "Test Flextables"
author: ""
date: ""
output:
bookdown::pdf_document2:
toc: false
fig_caption: yes
latex_engine: xelatex
number_sections: false
keep_tex: true
pdf_document: default
html_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(flextable)
library(bookdown)
library(knitr)
TEST_TABLE <- structure(list(`Winter Feeding Strategy` = c("Shallow snow terrestrial lichen",
"Shallow snow terrestrial lichen", "Shallow snow terrestrial lichen",
"Shallow snow terrestrial lichen", "Shallow snow terrestrial lichen",
"Deep snow arboreal lichen"), `Ecotype Name` = c("BC Northern Alberta Mountain",
"BC Northern Alberta Mountain", "BC Northern Alberta Mountain",
"BC Northern Alberta Mountain", "BC Northern Alberta Mountain",
"BC Mountain"), Location = c("Northern BC", "West central BC",
"North central BC", "East central BC", "West central Alberta",
"Southeastern BC"), `Nationally Significant Population by National Ecological Area (SARA)` = c("Northern Mountain",
"Southern Mountain", "Southern Mountain", "Southern Mountain",
"Southern Mountain", "Southern Mountain"), `COSEWIC Designatable Unit (2011)` = c("Northern Mountain",
"Northern Mountain", "Northern Mountain", "Central Mountain",
"Northern Mountain", "Southern Mountain"), `Southern Mountain Caribou Groupings` = c("Not Applicable",
"Central Group", "Central Group", "Central Group", "Central Group",
"Southern Group")), row.names = c(NA, -6L), spec = structure(list(
cols = list(`Winter Feeding Strategy` = structure(list(), class = c("collector_character",
"collector")), `Ecotype Name` = structure(list(), class = c("collector_character",
"collector")), Location = structure(list(), class = c("collector_character",
"collector")), `Nationally Significant Population by National Ecological Area (SARA)` = structure(list(), class = c("collector_character",
"collector")), `COSEWIC Designatable Unit (2011)` = structure(list(), class = c("collector_character",
"collector")), `Southern Mountain Caribou Groupings` = structure(list(), class = c("collector_character",
"collector"))), default = structure(list(), class = c("collector_guess",
"collector")), delim = ","), class = "col_spec"), class = c("spec_tbl_df",
"tbl_df", "tbl", "data.frame"))
```
## Test Table No Fitting
```{r TEST1, echo=FALSE, message=FALSE, warning=FALSE}
TEST_FLEX<- flextable(TEST_TABLE) %>%
merge_v(1:6)%>%
theme_zebra() %>%
border_inner_h()
TEST_FLEX
```
## Test Table autofit()
```{r TEST2, echo=FALSE, message=FALSE, warning=FALSE}
TEST_FLEX<- flextable(TEST_TABLE) %>%
merge_v(1:6)%>%
theme_zebra() %>%
border_inner_h()
autofit(TEST_FLEX)
```
## Test Table set_table_properties
```{r TEST3, echo=FALSE, message=FALSE, warning=FALSE}
TEST_FLEX<- flextable(TEST_TABLE) %>%
merge_v(1:6)%>%
theme_zebra() %>%
border_inner_h()
set_table_properties(TEST_FLEX, layout="autofit")
```
