I don't think that the quote is particularly worrying.

I think the FBI lawyer is pointing out that as the scope of what constitutes a search expands the harder it becomes to establish probable cause in the first place.

I agree with the article, that if 90% of the affected GPS trackers could demonstrate probable cause to get a warrant then the FBI doesn't really have cause to complain (about this one ruling). However, I don't think that invalidates the quote.

I think the quote is literally true and shouldn't be taken as anything but a FBI lawyer talking about the limitations that the agency faces but like the article says the limitations aren't necessarily a bug.

Edit: Clarity