I think this is about the fact that a multibranch project (or GitHub Organization project) checks out the same repo for each branch or pull request multiple times, apparently without making use of git's ability to share hardlinks between local git clones.
I'm more familiar with GitHub Organization jobs, but I think it would be similar with Multibranch. Please forgive me if I use some of the wrong terms.
1. User creates a GitHub Organization job folder
2. Jenkins creates a GitHub repository folder for each repo
3. Jenkins creates one pipeline job for each branch or pull request, within that repo, which contains a Jenkinsfile (depending on the settings of the Organization job folder)
Every time a node is allocated by a pipeline job and runs checkout scm, it appears to clone a copy of the repository directly from GitHub, thus using disk space (and bandwidth) proportional to the number of branches.
I think the idea is that the primary git clone on the node should be associated with the repository as a whole (#2), and then the individual branch jobs (#3) would use a local git clone (git clone ../primaryGitClone), thus taking advantage of hardlinks for the files under .git/objects/. It would also be possible for these local git clones to fetch from the primary git clone to save network traffic.
A more advanced option would be to use git worktree so that there is actually a single git clone with multiple working directories, although the limitations of git worktree could make this tricky.