Edit the applicable xml file (/config/plugins/dockerMan/templates-user) and change the line that says
<TemplateURL>......</TemplateURL>
to be
<TemplateURL>false</TemplateURL>
and the items which are being re-added to the template during updates won't happen again, and FCP will also no longer complain.
There is. Toss the templates into /boot/config/plugins/community.applications/private/nameOfRepo/appName.xml Now any custom templates etc will show up within a category (if they're set), or also within the Private category
But, you'd still wind in with the same issue in FCP since it can't determine which you've installed, and assumes that linuxserver/mariadb is the template present in FCP without changing that line above