I leave my pump running even when I'm in the plunge and I definitely feel it not letting me build up a heat barrier. Keep in mind that while you sit in the plunge the water temperature will start rising. This will cause my chiller to turn on but if you bypass the chiller it won't be able to offset the temp increase. This might not be an issue for you.
The smaller filter housings do restrict the flow quite a bit I believe. Here is a guy that did some testing: https://www.youtube.com/watch?v=UPiR30vWGaI
That's why I went with a whole house filter housing in order to not restrict it as much. But that could be pointless if the chiller is what's restricting it the most!
For measuring flow I filled a bucket to a known amount of water and timed it. I did it about 5 times and averaged it.