Allocation being fast isn't very important if you don't spend a significant portion of your time allocating. Isn't it possible that some languages (maybe even Go) by the nature of their semantics spend significantly less time allocating than other languages, and so tuning a garbage collector for latency is the appropriate decision?
Why do you seem to believe that the Go application has been tuned more to avoid allocations than the Java application? If it hadn't been, then you would have to agree that tuning the garbage collector for latency is better because you can invest some effort into your application to have it perform better on both throughput and latency.
Or is the argument that because "[throughput] is typically what applications want", this application is not a good example of most applications (according to what measure of "most")?