base解决方案：

split <- lapply(df, \(x) unlist(strsplit(replace(x, x == '', NA_character_), '\\+')))
as.data.frame(lapply(split, `[`, 1:max(lengths(split))))

        G1      G2    G3
1  GH13_22 GH13_22  GH13
2     CBM4    <NA> GH1O9
3    GH109    GT57  <NA>
4      PL7    GH15 CBM34
5      GH9     AA3  GH13
6     GT57    GT41 CBM48
7      AA3      PL  GT41
8     <NA>     PL2  GH16
9     <NA>    <NA>  CBM4
10    <NA>    <NA> CBM54
11    <NA>    <NA> CBM32

separate_rows()已被separate_longer_delim()取代，因为它与其他独立函数的API更加一致。被取代的函数不会消失，但只会收到关键错误修复。https://tidyr.tidyverse.org/reference/separate_rows.html
1.我们以长格式提供数据
1.使用dplyr中的na_if将空白替换为NA
1.使用这行代码summarise(cur_data()[seq(max(id)), ])，我们将每个组的id扩展到最大值。
1.最后，我们将准备好的数据框架向后旋转：

library(dplyr)
library(tidyr)

df %>% 
  pivot_longer(everything()) %>% 
  separate_longer_delim(value, "+") %>% 
  mutate(value = na_if(value, "")) %>% 
  group_by(name) %>% 
  mutate(id = row_number()) %>% 
  summarise(cur_data()[seq(max(id)), ]) %>% 
  pivot_wider(names_from = name, values_from = value) 

      id G1      G2      G3   
   <int> <chr>   <chr>   <chr>
 1     1 GH13_22 GH13_22 GH13 
 2     2 CBM4    NA      GH1O9
 3     3 GH109   GT57    NA   
 4     4 PL7     GH15    CBM34
 5     5 GH9     AA3     GH13 
 6     6 GT57    GT41    CBM48
 7     7 AA3     PL      GT41 
 8     8 NA      PL2     GH16 
 9     9 NA      NA      CBM4 
10    10 NA      NA      CBM54
11    11 NA      NA      CBM32

另一个选项，灵感来自this post中的@Peter M

library(tidyverse)
library(stringr)

# finds which vector is the longest and pads the other vectors accordingly
makePaddedDataFrame <- function(l){
  maxlen <- max(sapply(l,length))
  data.frame(lapply(l,\(x) x[1:maxlen])) # pads vectors with na
}

df %>% 
  mutate(across(.fns = function(x) str_split(x, pattern="\\+"))) %>% 
  lapply(function(x) do.call(c, x)) %>% 
  makePaddedDataFrame %>% 
  replace(is.na(.), " ") # if you want empty strings instead of na

        G1      G2    G3
1  GH13_22 GH13_22  GH13
2     CBM4         GH1O9
3    GH109    GT57      
4      PL7    GH15 CBM34
5      GH9     AA3  GH13
6     GT57    GT41 CBM48
7      AA3      PL  GT41
8              PL2  GH16
9                   CBM4
10                 CBM54
11                 CBM32