I will answer your questions here for the benefit of others;
Firstly, I would copy mediacenter-osmc to mediacenter-next-osmc. Then change
build_in_env to reflect the new directory name.
The reference to the specific commit is because Isengard is a branch (and thus a moving target). We prefer to pin the upstream and then apply our own patches. This makes it very easy to track changes and get no unwanted surprises.
You will also want to change API_VERSION=15 to ensure you are getting the correct language files.
You should change this commit tag to pull upstream, but do not just change it to 'master.tar.gz', change it to a specific commit. If you use Git correctly, you will be able to work out what builds were produced on which day which makes for easy tracking. You'll also be able to build an identical build, or an almost identical build with just one change etc.
There is now newclock5: https://github.com/popcornmix/xbmc/tree/newclock5. Indeed, removing the backport patch and adding the newclock5 one will work. There may be times when OSMC commits won't apply cleanly afterwards, but I can help with that.
You also asked if it's OK to have newclock5 in the directory and not affect Vero builds. Provided that the newclock5 patch is appropriately prefixed (rbp-xxx-SOME_PATCH_NAME.patch), then it will only be applied for that device. The only patches that are applied universally are prefixed with 'all'.
Hope this helps and let me know if you have any questions