With a physical attack the 'energy' payload can be very dense and targeted, and it can use adaptive computations to decompress based on local information, harness energy from the local star, do physical manipulations, etc.

This is an interesting point. However, while it is true that a physical attack can be precisely targeted, it is also true that it must be precisely targeted. One of the advantages of a SETI type attack is that it can be launched with no specific target in mind at all. The quadratic drop-off in signal strength that you allude to comes with a corresponding cubic increase in coverage space/volume, provided you run the signal continuously.

There is related analysis showing that sending particles or physical objects at high speeds can beat photons for interstellar communication in terms of energy efficiency.

This is an interesting point. However it would seem to apply to a targeted, point-to-point communication whereas a signal would not need to be precisely targeted.