If I'm reading this file correctly:
...
my $templatePath = $domain->prop('TemplatePath') || 'VirtualHosts';
...
You should be able change only your owncloud domain like this:
1) copy everything from the default virtualhost template folder to a new folder
2) Add the new template fragment in the Owncloud folder
3) set db variable for TemplatePath for your owncloud domain
4) signal-event remoteaccess-update
cd /etc/e-smith/templates/etc/httpd/conf/httpd.conf/
'cp' -r VirtualHosts/ Owncloud/
cd Owncloud
echo ' Header always add Strict-Transport-Security "max-age=15768000; includeSubDomains; preload"' > 04StrictTransportSecurity
db domains setprop owncloud.blah.tld TemplatePath Owncloud
signal-event remoteaccess-update
* The 'echo...' line goes off the screen to the right (on my system)
* Replace
owncloud.blah.tld with the domain name you use for owncloud
* Un-do using
db domains delprop owncloud.blah.tld TemplatePath
signal-event remoteaccess-update