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I believe their point was that they want to track their traffic, but when they use a third party like Google, Google provides tracking services for SpiderOak, Google also tracks you as well, which SpiderOak has no control over.

With it in house it is under their control: they can anonymize it, not collect certain information, they can't cross index it with your traffic from other sites, etc.

Google likely (or at least theoretically) has the capability to track the user across all the sites that use GA. In-house tracking doesn't allow this.