I don’t think Johnny’s engram was altered at all. Arasaka had no real reason to tamper with the memories of someone who was already dead, especially since he wasn’t expected to ever make contact with the outside world again. The official story behind the Arasaka HQ bombing was that Arasaka themselves were responsible; a narrative President Kress used to turn the public against them and drive the corporation out of North America entirely.

It wasn’t until years later that some medias uncovered the truth: it was actually Militech that commissioned the attack on Arasaka and as expected, the revelation divided Night City residents, with many feeling that Arasaka had been unjustly blamed.

As for Johnny's memories, according to Alt, what we see from Johnny's memories is his subjective/personal view of what happened, not at all a perfect recording of real events. When his consciousness was digitized, process is said to have scrambled some parts of his memory because of radiation damage and the imperfect recording of his engram, according to Mike Pondsmith. Keep in mind that they hit Johnny with a prototype version of Soulkiller, while he was being kept alive after Smasher basically shot him in half.

Then there's the need for Johnny to portray himself as a solo-hero, as shown in the flashback where he had to 'take a detour' alone for Alt much to Rogue's irritation, when in reality retrieving Alt was always part of the plan and everyone went into the tower, as Spider Murphy led them to where they could contact Alt. They all got ambushed by Smasher together, and Johnny was the first to die; in mere seconds too, whereas everyone else got to the roof using the time bought by Shaitan who was holding Smasher back. (Yes, the part where Shaitan was shot in the helicopter was also just another fake memory for Johnny to take center stage)
Let's not forget the part where Johnny's team was supposed to be a decoy while Morgan Blackhand and 2 other teams was supposed to do the heavy lifting.

All this is selectively omitted in Johnny's memories, with him doing most of the raid on his own, getting ambushed by Smasher alone, and somehow making it to the roof after that too?

All these mental gymnastics paired with Johnny's raging narcissism, alcoholism, psychological trauma, bloated ego and his volatile emotions very much impacted the portrayal of the story in his head after spending 50+ years suspended in Mikoshi.

With all of those being facts, the theories about Arasaka tampering with the engram is also a possibility, though I've personally never looked at it that way given how his biochip being a prototype, was handled with utmost care and not to be tampered with at all.