They explain it in the game (the being a super hero thing), and it is not a lore contradiction. They are not super heroes, they are a rogue faction that split from the original BoS to fight the remaining hostile mutants. They didn't get any support from the BoS Elder Council and even received bad criticism:I think from my dim memory that in addition to the whole treatment of the BOS as superheroes, they have one of the main characters being the big asshole BOS from the first game despite the fact he'd be dead or an old man as a major character.
Mind you, I think I have less issue with F3 because I consider Bethesda's take on it to be an alternate universe/soft reboot.
Now that I think about it, even the FO3 BoS was copied from a previous game, F:BOS .Before 2208, Rhombus created a splinter faction of the Brotherhood of Steel, despite some criticism from the elder council because of the former expedition grown by similar ambitions (to track down and assess the extent of the remaining super mutant threat) and the ensuing incident that divided the Brotherhood. He then starts a crusade against the largest faction of super mutants currently existing in the west, the Attis Army.
With some scribes and paladins, he mounted a new expedition which was later named the "Texas Expedition" and began tracking Attis' Army. They followed the army's trail to Texas and there, he discovered the vault prototype, an abandoned vault prototype dedicated to the Secret Vault project and installed themselves as the main base of the Brotherhood of Steel in Texas.
In 2208, Jane, the raider matron and their contact in the town of Carbon, reported movement of super mutants, and therefore Rhombus decided to go to Carbon with a group of paladins. Her information indicated their next destination, the ghoul city of Los. Here, Rhombus ends up being alone, captured, with all his comrades being killed in a bloody battle with super mutants and a local ghoul cult known as the Church of the Lost, but he managed to steal a keycard of the Secret Vault, the final destination of the Attis army and hid it under a truck. Rhombus is tortured by the cult leader, Blake, but later liberated by the Initiate. Afterward, Rhombus assisted the Initiate in getting to the truck where he had hidden the keycard. Once at the destination however, he is blown up by a ghoul suicide bomber.
Unable to continue fighting, he gives the Initiate the keycard and entrusts him with the task of stopping Attis' army and finding the Secret Vault entrance. Rhombus is left sitting near the truck, wounded. However, if the Initiate returns to the place later, Rhombus is nowhere to be seen. His fate is unknown.
About Rhombus being alive. The Vault Dweller is also still alive by the time of F:BOS (it's the year he leaves Arroyo) and the Vault Dweller is implied to be 27 years old when Fallout 1 starts. So Rhombus can be around that age in Fallout 1 and still be alive by 2208 (around the age of 70).
He is already quite old in F:BOS ingame too: