Packages
Finder can display a directory as one document or app. Its internal structure is managed by the owning software.
Symbolic links
A small link points to another path. Removing the link normally does not remove the target, but applications may require it.
Hard links
Multiple directory entries can refer to shared file data. Space is recovered only when the last relevant link is removed.
APFS clones
Copies can initially share physical blocks and diverge as data changes. Their logical sizes can exceed the additional physical space they consume.
Sparse files
Logical size can be much larger than allocated storage.
These structures explain why displayed file totals do not always equal reclaimed disk blocks. Avoid modifying package internals or links you do not understand.