Lots of variables there. It could be as simple as the impellor on the electric pump not being able to build as much pressure despite it's ability to flow very quickly. When you empty the system, there's little restriction. When you run through the block/plate it can offer significant restriction.
It could also be that the pump simply doesn't flow as much as the stocker does at engine speed. Again, without proper data it's as good as shooting in the dark. If the pump doesn't flow as much, then by the time you build enough pressure to work it may not flow enough to clear the block fast enough to deal with the heat. Hopefully it's the former vs the latter, as the latter would indicate that the electric pump you got was a step down from the OEM unit.
Without measuring the pressure built up in the block by the pump side-by-side with the stocker, as well as comparing flow at various operating RPMs it's near impossible to say what the cause really is.
That's the hard part with the too-fast-to-cool myth, every observable piece of evidence suggests that it's flow speed. The reality is that pressure is a bigger driver, but pressure isn't as readily observable. That's why I really don't take issue with folks thinking it's flow speed, because there's no way to demonstrate it with the instrumentation normally found on an engine.
I won't get into electric vs mechanical pump drives. Both have their place and only one can keep water circulating with the engine off for racing applications.
