There is no definite answer for this, as this is largely a matter of style. But I can give a few pointers.
Nearly all to follow is based on or from Trimble, J.R. (2000). Writing With Style: Conversations on the Art of Writing. 2nd ed. Upper Saddle River: Prentice Hall.
We vs You
The advantage of we is that it promotes a personal relationship between the speaker (author) and audience (a sense of togetherness, if you wish). This may or may not be desirable.
Although in the book the author uses we, there is a section that explains why "Never refer to the reader as 'you'" is a superstition (although the context is the alternatives of never referring to the reader, or refer to her as 'the reader'; we was not discussed there).
Although partially cultural, consider the differences between these two within an every day context:
Where did you leave the keys?
Where did we leave the keys?
You might be doing something wrong here.
We might be doing something wrong here.
The point is that you may come across as pointing, where we carries a bit more of a collective tone.
My personal verdict would be to use we.
Passive vs Active voice
The book is much more definite on this. It states:
Active verbs move us forward; passive verbs move us backwards. Active verbs give the actor up front; passive verbs make us wait to learn the actor.
Also notice that neither in:
In this chapter service X will be configured
This option can be omitted because feature Y is not used
any human is being involved - the phrasing is rather cold and technical.
Since it's a UX forum, and since the hot trend at the moment is emotional design, you can easily see the benefit of we or you.
I believe the argument here is in great favour of your first proposal:
In this chapter we will configure service X...
This option can be omitted because we don't use feature Y.
But, it's still a matter of style - it's about how you want to come across to your target audience.