> “Consists of” may be OK (any native speaker around, though?).

"Consist in" means "To have the thing mentioned as the only or most
important part." [1]  "Consist of" is usually about several things [2],
AFAICT.

Which one should I use?

> “Preserving” instead of “honoring” changes the meaning.  The intended
> meaning of the sentence was that the system would automatically install
> any dependencies, or, if building from source, install any build time
> dependencies.  What did you mean?

I meant the same.  Should I keep "honoring"?

> Actually, documentation-wise, my wish would be for people to primarily
> focus on those parts of the manual that are *not* written yet.  :-)

Which parts would you like to see documented before the next release?

[1] https://en.wiktionary.org/wiki/consist_in
[2] http://idioms.thefreedictionary.com/Consist+Of