Should be able to get away with two sets of configs vs seperate set for each OS. Updated install and updater scripts as well.

globalblacklist.conf

@@ -58,7 +58,7 @@
 	#		<Directory /var/www/html>
 	#			AllowOverride All
 	#			Options FollowSymLinks
-    	#     		Include /etc/apache2/custom.d/globalblacklist.conf
+    	#     		Include custom.d/globalblacklist.conf
   	#		</Directory>
 	#	</VirtualHost>
 	# ********************************************************
@@ -699,7 +699,7 @@ BrowserMatchNoCase "^(.*?)(\bZyBorg\b)(.*)$" bad_bot
 	# Include your Own Custom List of Bad User Agents
 	# ***********************************************
 
-Include "/etc/apache2/custom.d/blacklist-user-agents.conf"
+Include "custom.d/blacklist-user-agents.conf"
 
 	# ************************************
 	# GOOD REFERERS - Spared from Checking 
@@ -713,7 +713,7 @@ Include "/etc/apache2/custom.d/blacklist-user-agents.conf"
   	# Read Comments inside whitelist-domains.conf for customization tips.
   	# Updating the main globalblacklist.conf file will not touch your custom include files
 
-Include "/etc/apache2/custom.d/whitelist-domains.conf"
+Include "custom.d/whitelist-domains.conf"
 
 
 # ****************************************
@@ -783,7 +783,7 @@ Include "/etc/apache2/custom.d/whitelist-domains.conf"
   	# Read Comments inside bad-referrer-words.conf for customization tips.
   	# Updating the main globalblacklist.conf file will not touch your custom include files
 
-Include "/etc/apache2/custom.d/bad-referrer-words.conf"
+Include "custom.d/bad-referrer-words.conf"
 
 	# ************************
 	# Bad Referer Domain Names
@@ -7192,7 +7192,7 @@ SetEnvIfNoCase Referer ~*zzlgxh\.com spam_ref
 	#		<Directory /var/www/html>
 	#			AllowOverride All
 	#			Options FollowSymLinks
-    #     		Include /etc/apache2/custom.d/globalblacklist.conf
+    #     		Include custom.d/globalblacklist.conf
   	#		</Directory>
 	#	</VirtualHost>
 	# ********************************************************
@@ -7270,7 +7270,7 @@ SetEnvIfNoCase Referer ~*zzlgxh\.com spam_ref
   	# Read Comments inside blacklist-ips.conf for customization tips.
   	# Updating the main globalblacklist.conf file will not touch your custom include files
   
-	Include "/etc/apache2/custom.d/blacklist-ips.conf"
+	Include "custom.d/blacklist-ips.conf"
 
 	Require not env bad_bot
 	Require not env spam_ref
@@ -7296,7 +7296,7 @@ SetEnvIfNoCase Referer ~*zzlgxh\.com spam_ref
   	# Read Comments inside whitelist-ips.conf for customization tips.
   	# Updating the main globalblacklist.conf file will not touch your custom include files
 
-	Include "/etc/apache2/custom.d/whitelist-ips.conf"
+	Include "custom.d/whitelist-ips.conf"
 
 	# ***********
 	# Google Bots