There is a pretty large hole for the linkage (on my car) and a rubber boot as well. Are you sure it's not a bushing? There are lots of possibilities in the rear suspension, and something that seems tight on a hoist, may not be with the weight of the car bouncing up and down on it. The other thing I've discovered (the hard way...) is how often sound travels from it's source to another apparent location.
I have a weird clunk when I start off (usually) that I'm having trouble locating too. I'm hoping it's not an engine mount. Let us know what you end up finding.
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