Created attachment 172544 [details]
I realized in my previous bug report linked, the fix was not complete.
The attached diff fully solves this issue by making the necessary files writable, not just by root but by owncloud's user (by default 'www') and by group members to follow the convention of other writable folders like /data and /config.
A commit references this bug:
Date: Mon Jul 18 01:39:01 UTC 2016
New revision: 418681
.user.ini and .htaccess should be writable by default user and group.
Submitted by: Joshua Ruehlig <joshruehlig at gmail.com>