Heller's characterization throughout the zones is an exact mirror to Alex's. In the Green Zone, he mostly cared about protecting the citizens of NY, like Alex in the end of the game. In the Yellow, he was mainly seeking revenge, and in the Red Zone, he only cared about saving a family member...
At first, you may think its pretty stupid of Black Watch and the Marines to just ignore a guy gliding down and landing right beside them in earth-shaken crater. Its obviously Heller or Mercer up to more shenanigans at their expense. But then the Orion project and "Evolved" are introduced and it makes sense. They expect superhumans among their rank popping in and out. Its why just standing there like you belong there after pulling a blatantly mutation-enabled stunt shrugs off suspicion instead of giving them more time to suspect you. They think you belong there.
But aren't they unaware of the Evolved in their ranks? And if they discover one, they try to kill them. And as for the Orion, they all seem to have those suits on, which you don't have. They shouldn't think you belong there at all.
One might wonder why Orion soldiers do not seem to have integrated viral detectors as per their original D-Code cousins. Remember how the initial D-Codes were brought in to combat serious infected threats, but specifically tuned for melee combat. In other words, to match the likes of Alex Mercer. Then recall how the main infection in the first Prototype was Elizabeth Greene's Redlight virus, or DX-1118A as it may be. D-Codes, set up for hunting down Alex Mercer using similar UAV detection technology, are configured to filter out Alex's strain instead, specifically the DX-1118C, or Blacklight. Only a few other creatures are of the Blacklight variant during the events of the first game, such as the "Evolved Infected"(read: Parkour Zombies) created from the Penn Station outbreak. This gave the D-Codes fairly infrequent false positives among the massive Redlight-based infection like the regular zombies and hunters.
Now fast-forward to Prototype 2: The infection of New York was restarted after the decline of Greene and Redlight in general, courtesy of Alex's role in using a much larger quantity of Blacklight than previously, that is to say his own internal storage. Same thing as before, but now everything is Blacklight instead of Redlight. Detectors still seemingly function as before, but the tactical application is diminished due to everything registering as Blacklight. This is of questionable usefulness to Blackwatch and Gentek if just about every infected signature is unlikely to be Mercer since he blends in among his own creations. James Heller is also Blacklight, therefore blending in as well.
Except... when there's a virus that can cause shape-shifting, and the organization whose detecting it is paranoid to the point of unquestioningly gunning down their comrades at the mere suggestion that "Hey, that's Mercer!", false positives should not be a problem; in fact, just being able to detect the infection would probably be useful when they are literally springing up from out of the ground. Being strong enough to contend with the infected in melee combat is hardly useful only in regard to Mercer. I'd say it's more likely that the reason they can't detect the virus is that the Orions were created by Doctor Koenig, who had a very good reason not to give the Orions that ability.
Except they can detect the virus. Numerous times, the radio chatter talks about someone detecting an increase in "infected biomass", although that usually means you're about to get swarmed by Brawlers or a Goliath is about to show up. Which would make one believe that you need a certain amount of infected mass to trigger the detectors at a distance, and something Heller's size has to get close before it can set off the detector. Another possibility is that there's a city-wide network of detectors to help them triangulate large concentrations of biomass and the various bases have a few detectors scattered around to make sure nobody's sneaking around inside.
It actually makes sense that, at least on the lower difficulties, Heller is able to take Mercer down- in the beginning of the game, Heller takes Mercer on in hand-to-hand combat and does quite well until Alex infects him. So of course when Heller (Who is a trained Marine) is on even ground with Mercer (A scientist who relies heavily on his powers) get into a fight, Heller would win.
The map works because Heller carries a Blackwatch smartphone that, as expected, contains a map of the entire city. It also shows Blackbox locations because it's built to pickup on their frequencies whenever they're supposed to be recovered, and gives field ops location if they ever need assistance.
Then one recalls that the only source material that sample vial of Blacklight could base itself on was a very sociopathic genetic scientist called Alex Mercer, who had in his final moments been very angry and chose to spitefully jeopardize the future of mankind.
After which his first several consumed minds were Blackwatch and Gentek personnel, hardly examples of sparkling paragons of virtue. There's also the fact that literally every set of memories he takes on involves dying horribly, at the hands of a the face he sees in the mirror. It's a wonder Mercer didn't get even more sociopathic as the first game went on.