ownCloud needs to be able to write to .user.ini to change the upload size if using PHP-FPM
ownCloud 9 appends to it's .htaccess upon installation (during lib/private/setup.php) if it sees the apcahe 'env' and 'rewrite' modules are available. This is needed to get "Pretty URLs" working properly.
I assume the fix should be something like, but I'm not exactly sure.
A commit references this bug:
Date: Thu Apr 14 14:51:12 UTC 2016
New revision: 413265
ownCloud needs to be able to write to .user.ini to change the upload size
if using PHP-FPM.
Submitted by: Joshua Ruehlig <joshruehlig at gmail dot com>