Rich Trouton covers the move of /Volumes to no longer being world writable as of Sierra (10.12)
https://derflounder.wordpress.com/2016/09/21/macos-sierras-volumes-folder-is-no-longer-world-writable/
As for your issue in writing to the VolumeConfiguration.plist, I don't see it listed in the rootless.conf but I don't believe that Spotlight indexes network drives by default (I'll have to check my notes on this).
With SIP enabled, the command "defaults read /.Spotlight-v100/VolumeConfiguration.plist" results in 'domain not found', however "cat /.Spotlight-v100/VolumeConfiguration.plist" shows the contents. With SIP disabled you can read and write to the plist using the defaults command, which confirms my suspicion that rootless.conf is not a live configuration file, but rather just a documentation list that may or may not be up to date with any given release.
Anyway, still looking for an alternative means of configuration.
@MrP I ran into this. I submitted feedback to Apple to allow mdutil
the option to manage exclusion paths for Spotlight index with the options of: add-path, remove-path, and reset exclusion and perhaps some support for reading from a plist. I'm not sure whether they'll oblige but you should submit similar feedback if interested. Also just so you know this is only a problem in 10.14. In 10.13, it seems to work fine.
@bpavlov
I submitted feedback as well. Thanks! Yeah, I have to re-certify all of our configurations every major os release, as I assume most do. Didn't see this until 10.14.