Maby, thats because "Matter" IS "Energy". Matter doesnt contain energy, it IS energy. Without energy, matter doesnt exist... It has been proven that there is energy even in vacuum empty space...But no matter...It takes some more energy to have matter. So, the total mass depends on the energy.

You know that, the more electrons you have, the more energy that element contains...And, heavier elements produce more energy in a nuclear-reactor...or when burning...or anything.
Its not really production, its a release of that energy. So, when a body hits something and it stops, it transfers all that energy (or mass gained through "Inertia", which is more like the change in speed, not withstanding a change in speed) to the other object, because of the impact, and it contains a lot less energy...therefore, a lot less mass.

I dont know if you're familiar with the formation of heavier elements, but its an interesting read... Through collision, upon the death of a star, two elements "join forces" (or Energy) and form a new element with a higher energy... So, from hydrogen, you get gold or even uranium...Thus, it gets heavier than hydrogen because of the energy. The light alone, or external forces giving energy to an atom arent enough to change its atomic weight, thats why you cant form new elements by shining a flash light on them...It needs a big collision with energy to join it.
A static block of iron isnt without energy. Its just, that, the energy is motionless. Energy isnt expressed solely by motion...

The equation just shows, that mass is energy. Or, more like, that mass is a fraction of the energy that is forming it, because it needs to be multiplied by the maximum speed possible (speed of light). By the way, stop thinking in meters per second or joules, these are just names and milestones for measurement. You cant define a starting or ending point for energy or for mass, because there are infinite possibilities beyond our measuring capabilities.

An atom is just a bundle of energy particles, as shown by recent tests and theories. And atoms form mass. What forms the energy particles and why is the bigger question

I hope this helps a little