As being discussed in #885, we need to improve the Package and Dependency relationships to support transitive dependencies.

During this, should a dependency tree be specific to a single project being scanned or shared across all the projects.
Say, for example:

purl A
    +------purl B
    +------purl C
                +------purl D

here, whenever and wherever we find purl A, we know - for sure - that the above dependency tree will be present. Same applies for purl C (purl D will always be a dependency) regardless of the project being scanned.

Would it make more sense to have a central dependency relationship mapping as the source of truth for entire SCIO that will be ever-evolving with every scan performed ?

There is one caveat to this approach, let's say purl C changes its dependency from purl D to purl E at some point of time after the scan was run. This breaks the entire hypothesis of having a central dependency mapping source of truth.
Ideally, purls should not change dependencies at points of time but we live in a weird world.