Yes, those internal resistors (especially the 500Ω one) and the embedded diode will throw off the B-E (nominally around 1.2V) and E-C measurements, respectively. And yes this diode-checker test is only a quick go-nogo test, it doesn't test the transistor's main ability: to amplify. (As an aside, there are those cheap multimeters with transistor check function. You still need to do the diode check of the junctions before you can trust these transistor checkers.)
Anyone seen a germanium darlington? Not sure if one exists...