wrote
One possibility is that those "thread" in the old water pump base may
not be "real" thread. They may be a corroded surface that mirrors the
thread in the bolt.

IOW, corrosion formed around the bolt threads creating something that looks
like a threaded hole. That sounds plausible enough for me.

Do we need to re-apply the heli-coil insert whenever we
replace the bolt (like when we need to replace the impeller)?

The coil will probably stay in there forever. I suppose it's possible for it
to back out when you remove the bolt, but I've never seen it happen.