VFD'd on the house circuit will do you no good, especially since there are 3-ways at the load points.

The 3-ways make for constant flow in the loop. You could utilize the vfd as a means to set the flow rate instead of using discharge valves.

Did anyone ever set the flow rates? Through the loop, or the chiller bundles?

To utilize a VFD properly, the loop volume needs to be variable, as it would be if the control valves at the loads were 2-way.

In either case, vfd's won't help with chiller cycling. For that, timers, buffer tanks, HGBP, or an APR valve would be needed.

Personally, I'd be looking at an APR valve added to the 1st stage compressor on each chiller module.