This is a simple case of "food for thought". Adding the half mask to Heavyarms during the last battle in Endless Waltz was likely baffling to many viewers. I also briefly wondered why the clown mask Trowa wears as part of his circus costume wound up being customized for his Gundam. (Part of me thought it was a shame it wasn't there the entire time.) I mean, isn't that just crying out, "Hey, the person piloting Heavyarms is the clown from the circus we went to a few days ago!" After a while, I came up with a theory.
When the clown mask is added to Gundam Heavyarms during the battle against Mariemaia's Army, perhaps it was to show that Heavyarms was no longer part of the Barton Foundation. It belongs to a seperate group: the Gundams pilots of the One-Year War. At the same time, perhaps the addition really was a way to declare who was piloting the Gundam. When I watch that scene again and consider what is happening in that moment, I believe the addition of the mask said: This is me. It reflected what all of the Gundam pilots and what the Peventers were doing right then: "I am (enter name here). I will stand up and fight to keep the freedom and peace I have obtained this past year."
In my first viewing I also found it odd that for all the effort put into making an enormous half mask for Heavyarms Kai, it fell off during battle. Later when the mask was shown to have fallen off the mobile suit, it also seemed to reflect the scene when he first appeared in Endless Waltz. When he left the circus tent to investigate the sketchy men looking in, he dropped his half mask. The civilian was put aside and the soldier stepped forward. Symbolically he casts away his civilian form and reveals what is beneath, a boy whose origins were the battlefield.
Therefore, yes, I believe the brief mask scene was very symbolic. He was using Heavyarms not as Pilot 03, not as a soldier known as Trowa Barton and not as a soldier under Mariemaia. He was but a civilian. Having Heavyarms wear the mask identified him as the young clown who performed at the circus with his friends and co-workers. It identified him as the nameless boy who was fighting for the home and normalcy he finally found.
'Tis merely a theory.