出现第一个问题是因为您在图表级别定义的工具提示格式化程序正在覆盖散点系列的工具提示格式。相反，您可以分别为每个系列定义工具提示以自定义它们。
对于您的第二个问题，抖动似乎是Highcharts中与箱线图一起使用时的一个已知问题，不幸的是，这个问题没有一个直接的解决方案。
您可以尝试以下解决方法，我们在系列列表本身中添加工具提示，并删除图表级别的工具提示：

library(highcharter)
library(dplyr)
library(gapminder)

ds <- gapminder %>%
  dplyr::filter(year == 2007) %>%
  dplyr::arrange(-pop)

myboxplotData <- data_to_boxplot(
  ds,
  lifeExp,
  continent,
  group_var     = continent,
  add_outliers  = FALSE,
  fillColor     = c("red", "green","yellow", "pink","blue"),
  color        = "black",                        
)

# Add tooltip to each series
myboxplotData <- lapply(myboxplotData, function(s) {
  s$tooltip <- list(
    headerFormat = paste0('<span style="font-size: 10px">', s$name, '</span><br/>'),
    pointFormat = '<strong>Continent : {series.name}<br/>Maximum : {point.high}<br/>Minimum : {point.low}</strong>'
  )
  s
})

highchart() %>%
  hc_chart(
    events = list(
      load = JS("function () {
        Highcharts.each(this.series, function (series) {
          series.legendSymbol.attr({ fill: series.options.fillColor });
        });
      }")
    )
  ) %>%
  hc_xAxis(type ="category") %>%
  hc_add_series_list(myboxplotData) %>%
  hc_xAxis(title = list(text = "continent")) %>%
  hc_yAxis(title = list(text = "Life expectancy")) %>%
  hc_title(text= "Boxplot using highcharter") %>% 
  hc_legend(enabled= TRUE) %>%
  hc_add_series(
      data = ds,
      type = "scatter",
      hcaes(x = "continent", y = "lifeExp", group = "continent"),
      tooltip = list(pointFormat = "Life Expectancy: {point.y}")
  ) %>%
  hc_plotOptions(scatter = list(
    color = "grey",
    showInLegend = FALSE,
    marker = list(
      radius = 6,
      symbol = "circle",
      lineWidth = 2
    )
  )) %>%
  hc_plotOptions(scatter = list(jitter = list(x = 0.05, y = 0)))

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这里是我的问题的解决方案，谢谢@madepiet的线索。要点是设置一个空的headerFormat，以便删除自动设置的序列的名称。
我使用了一个“for循环”来设置箱形图的工具提示，因为lapply（第一个madepiet的答案）会给我一个错误。

library(highcharter)
library(dplyr)
library(gapminder)

ds <- gapminder %>%
  dplyr::filter(year == 2007) %>%
  dplyr::arrange(-pop)

continent_colors <- c("red", "green","yellow", "pink","blue")    

myboxplotData <- data_to_boxplot(
  ds,
  lifeExp,
  continent,
  group_var     = continent,
  add_outliers  = FALSE,
  fillColor     = continent_colors,
  color         = "black"                        
)

mylist <- list()
for (tmp in myboxplotData$data) {
  name <- tmp[[1]]$name
  high <- tmp[[1]]$high
  low <- tmp[[1]]$low
  lst <- list(
    headerFormat = '',
    pointFormat = paste0('<strong>Continent : ', name,'<br/>Maximum : ',     high,'<br/>Minimum : ', low, '</strong>')
  )    
  mylist <- append(mylist, list(lst))
}
myboxplotData$tooltip <- mylist

highchart() %>%
  hc_chart(
    events = list(
      load = JS("function () {
        Highcharts.each(this.series, function (series) {
          series.legendSymbol.attr({ fill: series.options.fillColor });
        });
      }")
    )
  ) %>%
  hc_xAxis(type ="category") %>%
  hc_add_series_list(myboxplotData) %>%
  hc_xAxis(title = list(text = "continent")) %>%
  hc_yAxis(title = list(text = "Life expectancy")) %>%
  hc_title(text= "Boxplot using highcharter") %>% 
  hc_legend(enabled= TRUE) %>%
  hc_add_series(
    data = ds,
    type = "scatter",
    hcaes(x = "continent", y = "lifeExp", group = "continent"),
    color=continent_colors,
    tooltip = list(headerFormat="", pointFormat = "Life Expectancy: {point.y}")
  ) %>%
  hc_plotOptions(scatter = list(
    showInLegend = FALSE,
      marker = list(
      radius = 6,
      symbol = "circle",
      lineWidth = 2
    )
  )) %>%
  hc_plotOptions(scatter = list(jitter = list(x = 0.05, y = 0)))

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