Are you using GlassFrog?
1. I think it is perfectly "legal" to have different repos; if there is no policy against it, you can use whatever you like. Further, you could create a policy constraining types of work to be recorded in different places.
Project work not included in the backlog must be listed in GlassFrog (or wherever).
[This may be a borderline valid policy...so you may need some accountabilities as well, not sure.]
2. In Holacracy, if something has a discrete endpoint, or is a result/outcome and takes more than one next action then it is a project, so yeah in those cases! Our dev team and others will list certain types of dev work in progress updates to share during tactical, but not every chore or story if that makes sense.
Project definition: http://www.holacracy.org/constitution#122