Short answer
Thanks for asking! 
If you’re talking about a Project in the way our command line tools refers to it, such as the “Project file” example of SourceCreds’.
This idea of a Project is the whole of the project.
- Which Discourse forum is used.
- What GitHub repositories are there.
- What Identity aliases to use between platforms.
- etc…
(There are plans to deprecate this Project term, and refer to this as a SourceCred instance instead.)
On the other hand Initiatives refer to concrete, finite work in a Project. Whether it’s in proposal stage, in progress or completed.
So a Project would be: Soucrecred is a Project.
And an Initiative could be: Create Discourse plugin
Projects can have many Initiatives.
In depth
Why finite? Initiatives are used to make it easier for people to fine-tune the SourceCred algorithm and give the proper weights to things they care about.
Reasoning about ongoing goals (like “have good documentation”, “be a friendly, supportive community”) is a different beast altogether, so it either deserves it’s own construct to value these in SourceCred (in my opinion). Or result implicitly from the concrete valuations in each domain. For example, if documentation related Initiatives are consistently given high weights, that means our community implicitly values the “have good documentation” goal.
On the other hand Initiatives being finite makes them familiar. Setting their weight is similar to defining priorities, or setting a Cred bounty.
What about concrete?
Note: by concrete I don’t mean concrete output! It doesn’t have to produce artifacts like code or documents. It can be related to social events or emotional labor. By concrete I mean, it has a (finite) scope and a description on-record. Something you can refer to. Something that can have a completion status.
This is important to be able to evaluate and in the future re-evaluate what this has contributed to the Project. In order to do that, we should be on the same page in terms of what we’re talking about. Hence concrete.
As an example: we can compare the value of these Initiatives.
Today I think the Discourse plugin is a lot more valuable than the Discord plugin.
- The CredSperiment has used Discourse a lot, and this plugin has been key.
- Discourse is also key in the possible beta partnerships following out of that.
On the other hand Discord has provided some value already and I would speculate has future value.
- Building a prototype at CredCon helped move things forward.
- MetaGame is running a prototype Discord plugin and is having a field day with it! (Awesome stuff!)
- We’ve started using #didathing and #props more with a Discord plugin in mind.
However things could very well change in the future. Discord has a massive user base. Perhaps by next year the tables turn and we might say the Discord initiative was much more valuable than the Discourse one. Who know?! Time will tell!
The point of that was to say, we can make arguable (and not needlessly emotionally abrasive) value comparisons now and in the future between Initiatives because they’re concrete.