The purpose of 'cloud transform' is to estimate projection of cloud shadows based on cloud position and sun azimuth. Or, as the author specifies it
// Project shadows from clouds for the distance specified by the CLD_PRJ_DIST input.
Then, if you want to display the cloud-free image, you need to apply all those masks using
Here is a result: https://code.earthengine.google.com/0701d40fb1f844cfd376e8e6cbd7d946
However, if you want to make a cloud-free composite, you have to map this function over many images and then reduce them into a composite (e.g. take median). Here is a result: