Sorry for the late response, I was away for a few days.
Turns out that all my problems (supposedly missing metrics) was actually just impatience on my side.
For me in my installation it became apparent that after changing discovery rules, I really needed to wait for an extended period of time (definitely more than 1 hour) AND restart all instrumented JVMs (although all are running on Oracle/Sun 8 JDK) to get reliable results.
After I did that (change rule, stop JVMs, delete all old BTs/ServiceEndpoints, restart JVMs) I now get repeatable and correct metrics. Well, sometimes they are a few tenths of 1 percent off in counting calls, but that's more than good enough for metrics!
So sorry if I did spread some FUD here, but for me it now looks that ServiceEndpoints now provide exactly the metrics I was expecting from them. They show basic KPI for all invocations of my service, even if it happened in the context of an already existing BT. Perfect!
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