Yes, typically the only way to measure Ze is to isolate the installation supply (usually via the incoming switch) so it is completely dead, and then disconnect the supply earth and measure to it, and put it back immediately. Removing the bond conductors might do it, but as you can have links from the installation CPC to extraneous metalwork via boiler CPC, immersion heater CPC, or supplementary bonding, etc, you can never be sure.
Measuring Zs is simpler as everything is still in place. Of course if the supply earth is faulty then you would risk raising the CPC and any extraneous parts with a high impedance to potentially dangerous voltages, but most MFT will usually throttle the test current if they see a voltage change that could exceed 50V to keep things reasonably safe.