The main thing is to use the right tool for the purpose.
Here, the purpose is to align the subject and image planes perpendicularly in respect to the optical axis, which is the direct line between the center of the sensor and the negative. This is best accomplished by using a mirror like so: How To Adjust for Low Distortion
Using a bubble level refers everything to the center of earth’s gravity - and every little deviation adds up to an alignment that is less than perfect in comparison.
The device you show is built to adjust two axis indeed and the third is done by slightly rotating the negative holder or lens or camera (bayonet mounts have some play) - or done in post. And in order to use the device to its full, it should go between the camera and the column (or the vertical board in my latest rig).
Using shims is a way to circumvent the need for additional elements and junctions, all of which add to the elasticity of the setup. Instead of the shims, I could have used the pole-height adjuster, but then, the whole installation will be more susceptible to vibration and flex. Directly attaching the rail to the vertical board creates a setup into which i can attach the camera with almost no need for further adjustments - except after removal and re-attachment of the camera cage.