ok you mention the domain so that it looks like its a sub domain and not a add on domain.
ftp.mydomaiin.com is a sub domain of mydomain.com
An add on domain would be a different domain name like mydomain2.com
The problem may then be piwik may have a problem as the location of teh sub domains folder is different than the main domains folder so definitely check the paths structure in the php files.
Normally a subdomain i would think if the js script is the same would end up being put into the data of the main piwik install. I think since this is a sub domain the whitelisting is the way they allow a sub domain to be separated and report like a seperate true domain.
If you are looking at providing a service of tracking various sites would it not be an option to have your one domain to host piwik. Create separate JS code for each site that would be placed on all the various sites and mange it from one piwik install?
Since the code is custom per site the domains would have not real relation that google would group to.
Even if you begin to host various web sites via cpanel since they are separate domains that scenario would work.
just putting options out there as since you specify a subdomain as part of your URL then it will be grouped in a sense by google to your main domain.