You first want to load your files into a list.

library("tidyverse")

# Load the data.
# Specify the directory with your tables.
# Change the delimiter to whatever your files use.

files <- list.files("path/to/dir", full.names=TRUE)
files <- set_names(files, basename(files))

example <- imap(files, function(x, y) {
  read_delim(x, delim="\t") %>% rename_with(~str_c(.x, y, sep="_"), !c(ChrID, position))
})

I'll create some example data of what to expect once your files are loaded.

example <- list(table_1.txt = structure(list(ChrID = c(1, 1, 1), position = c(100, 
200, 300), methy_table_1.txt = c(1, 1, 0), unMethy_table_1.txt = c(1, 
0, 1)), row.names = c(NA, -3L), class = c("tbl_df", "tbl", "data.frame"
)), table_2.txt = structure(list(ChrID = c(1, 1, 1), position = c(100, 
200, 350), methy_table_2.txt = c(1, 0, 0), unMethy_table_2.txt = c(1, 
1, 1)), row.names = c(NA, -3L), class = c("tbl_df", "tbl", "data.frame"
)))

> example
$table_1.txt
# A tibble: 3 x 4
  ChrID position methy_table_1.txt unMethy_table_1.txt
  <dbl>    <dbl>             <dbl>               <dbl>
1     1      100                 1                   1
2     1      200                 1                   0
3     1      300                 0                   1

$table_2.txt
# A tibble: 3 x 4
  ChrID position methy_table_2.txt unMethy_table_2.txt
  <dbl>    <dbl>             <dbl>               <dbl>
1     1      100                 1                   1
2     1      200                 0                   1
3     1      350                 0                   1

Combining is now a simple matter of reduce and full_join.

merged <- example %>%
  reduce(full_join, by=c("ChrID", "position")) %>%
  mutate(across(where(is.numeric), ~replace_na(.x, 0)))

> merged
# A tibble: 4 x 6
  ChrID position methy_table_1.t… unMethy_table_1… methy_table_2.t…
  <dbl>    <dbl>            <dbl>            <dbl>            <dbl>
1     1      100                1                1                1
2     1      200                1                0                0
3     1      300                0                1                0
4     1      350                0                0                0
# … with 1 more variable: unMethy_table_2.txt <dbl>