AutoSSL & Django Issue

Hello, I did a lot of searching but could not find a thread that spoke specifically to my problem. So forgive me if there is a duplicate somewhere. I recently had the AutoSSL plugin enabled on my KnownHost VPS running WHM v58 build 32 cPanel. I configured the plugin to use the Let's Encrypt service for SSLs. My server configuration has three different type of webpage setups running on Apache : 1) A few domains using normal HTML and .htaccess type config with "each domain set up as a unique user". 2) A group of sub-domains parked under a single primary domain user id. (all running html pages and .htaccess) 3) A few domains using Django to serve the website (no .htaccess but settings in apache virtual conf files) with "each domain set up as a unique user". Setup group 1 had no problem enabling the Let's Encrypt SSL certs through your plug in. I enable it and do a check domain and the log shows that a cert was needed and it is installed. I then see the .well-known/acme-challenge folder in the public_html folder. There are files in the folder initially but then disappear. HTTPS seems to work on these domains with no issue. Setup group 2 is only able to be configured if I enable AutoSSL on the User ID that all the sub-domains sit under. AutoSSL then tries to enable certs for it and all sub-domains. I only wanted a select group of these sub-domains to have SSL certs. From what I understand that is in future versions of your plugin you will allow this to happen? Or will your plugin always enable certs for all these sub-domains or not? I heard there was a feature request for this? Can you verify? Setup group 3 is the one having the real problem. When I try to enable AutoSSL on a domain configured with Django I get the following error:
WARN The domain "x.com" has failed domain control validation (The system queried for a temporary file at """ target="_blank" class="externalLink ProxyLink" data-proxy-href="http://x.com/15136.BIN_AUTOSSL_CHECK_PL__.HD758vMuXhQNdjx5.tmp"" rel="nofollow">http://x.com/15136.BIN_AUTOSSL_CHECK_PL__.HD758vMuXhQNdjx5.tmp", but the web server responded with the following error: 404 (NOT FOUND). A DNS or web server misconfiguration may exist.). at bin/autossl_check.pl line 449.
I looked in this forum and found some tricks about putting a RewriteCond %{REQUEST_URI} !^/\.well-known/acme-challenge/ setting in the .htaccess file. Django doesn't use .htaccess but can be configured via a virtual conf file inside Apache. I added that line along with RewriteEnging on. The problem persisted. Also, I notice that the .well-known folder is never created. I do want to note that my Django has the WebRoot folder changed from public_html. Instead the root of the domain is /home/userid/public_html/d18p275/domain_com/. Additionally actual webpage files that are served are in a "templates" folder off of the WebRoot. Lastly, you have to actually define URL entries in a urls.py file on you get a 404. Since your "temp" file seems to be dynamic in nature and I see no way to point you to the correct root folder where files are served from, I am not sure how to get AutoSSL working on my Django domains. Can you help me on how I get this working? Thanks...