Why are empty pylons weighed down?
Your reason 1 is correct. Without the ballast the aircraft would become a taildragger.

Why not pallets? This would produce the same center of gravity location, but a different mass distribution. Clearing this configuration even for being loaded and pushed around is more effort than simply placing the ballast where the mass of the engines would go. Now all clearances are valid and the aircraft can be handled much as one with the engines in place.

Next, engines are only installed shortly before delivery or first flight. The cost of capital is too high to install them any sooner.

(airbus.com) Example of clearances that would be affected by non-standard mass distribution.