TOML sucks for list of tables simply because they intentionally crippled inline tables to only be able to occupy one line. For ideology reasons ("we don't need to add a pseudo-JSON"). Unless your table is small, it's going to look absolutely terrible being all crammed into one line.

https://github.com/toml-lang/toml/issues/516

The official way to do list of tables is (look at how much duplication there is)

  [[main_app.general_settings.logging.handlers]]
    name = "default"
    output = "stdout"
    level = "info"

  [[main_app.general_settings.logging.handlers]]
    name = "stderr"
    output = "stderr"
    level = "error"

  [[main_app.general_settings.logging.handlers]]
    name = "access"
    output = "/var/log/access.log"
    level = "info"

vs

  handlers = [
    {
      name = "default",
      output =  "stdout",
      level = "info",
    }, {
      name = "stderr",
      output =  "stderr",
      level = "error",
    }, {
      name = "access",
      output =  "/var/log/access.log",
      level = "info",
    },
  ]

I would still reach for TOML first if I only needed simple key-value configuration (never YAML), but for anything requiring list-of-tables I would seriously consider JSON with trailing commas instead.