No, trackers are allowed as per their policy and exempted from officially considering it as an alteration. Provided the tracker is installed under supervision of a 3S or allowed and informed to them. Any sort of service that Atlas workshop can perform themselves as well is not considered. For example if you ask a 3S to install HIDs, they dont do that hence considered as out of company alteration. They dont install amps and subwoofers or change to non oem speakers even. But if you ask them to replace your old oem speakers to new ones, they do that.
These other additions also usually dont play any role in malfunction of other things, but an excuse is an excuse for the manufacturer. They just need a reason to deny you service for which they consider these alterations as things that can void warranty.