I think I've seen it done like that

  --option flag1,flag2

Another possibility is to make the main option an argument, like the subcommands in git, systemctl, and others:

  command option --flag1 --flag2

> --option flag1,flag2

Embedding a second parse step that the first parser doesn't deal with is done, but it's a rough compromise.

It feels like the difficulty in dealing with

  [--option [--flag1 --flag2]]