First some corrections:
- I did not update these files "mindlessly" or out of "religious dogma". You may have ditched Apache, but I have not and as a user of your software I actually appreciate the bundled .htaccess files, and consider them an extra safety net.
- You mentioned ownCloud. If I'm not mistaking they also still bundle .htaccess files in addition to the warning message you mentioned.
- I do not feel that the Apache syntax changes that often. And they did take care of backwards compatibility by supplying the module mod_access_compat.
That said, regarding your wish for a more comprehensive solution, I completely understand it. Another argument to move away from .htaccess files is that the default setting for AllowOverride has changed in Apache 2.4 from All to None, meaning that .htaccess files are by default ignored now. Also, I understand it is difficult for you to test my patch when you're not using Apache.
So, do as you see fit. Thanks for your great software.