Sorry but emacs package managers don't get in your way anymore than the bundled libraries that come with emacs. They often have bugs/limitations you may have to hack around. But you can't modify them if they are globally installed with different permissions/read-only fs. In past i had to work around the tls client not having parameters for client certs by using advice hooks.

But you can easily jump around very deep into packages and compile them with few changes to suit your need. Your last resort is advice(https://www.gnu.org/software/emacs/manual/html_node/elisp/Ad...). Most of the time you don't need to and they have roughly the same benefits of your distro maintained packages vs you vendoring and compiling your own little world.