With the new --init-directory
switch of Emacs 29, you can define a completely separate environment for Emacs that could be used to make more mean, lean and specialized versions of Emacs. For example, instead of having your Emacs do everything, IRC, email, programming, Org mode stuff etc. etc. etc. you could have a shell command invoking each one, e.g. Eirc, Eemail, Eorg, etc.
The configuration of bookmarks is just a file. You can edit it or even delete it.