I used wall plates. I think it's neater but it's a matter of perspective I suppose.
There is no discernible loss in properly connected cable lengths. Use solid runs if you can so you never have to worry about the splice getting loose, but if it's done well, even that risk should be next to zero.
More important is the total distance of the run. Use a sufficiently heavy gauge for the length you are going and you will have no problems.
As you say, face plates negate the worry about extra length. That is another good reason to go that way since you are starting fresh and have the opportunity. I just used open lengths when we built the house but face plates when I turned a room into a HT room. I am much happier with the wall plates.
Face plates do not negate the signal path. Nothing a human will ever detect anyways. Just be sure the face plate has a good, solid connection to the wire and you have no worries.
Sounds like you already have all the answers you need. A well labeled master face plate is indeed the way to go. As mentioned, I have both scenarios in my home. Trust me. Face plates are the way to go when you have this great opportunity to do it from scratch.
Caveat.
Your question was strictly audio & speaker wire so I stand firm on my answers. However, if you are doing a HDMI run, it is a rather finicky technology. I'm not promoting the expensive HDMI cables that falsely claim better picture quality and such. However, it can be distance sensitive and requires some forethought in installation.
