When you run make it follows the instructions in the Makefile; which is designed to install all the relevant plans, overlay all the overlays and run all the relevant conf.d scripts. So there is no way to make without doing that stuff...

Having said that you can undo the last step of a complete build by undecking build/root.sandbox and removing the build/stamp/root.sandbox

deck -D build/root.sandbox
rm build/stamp/root.sandbox

You can also do that to root.patched too; that makes it much quicker to redo...