Dr. Soong underlines that the Androids are 100% identical in hardware and have only a "slight" difference in programming. Then when Lore gets the emotion chip suddenly "those circuits" were NOT compatible to him and only properly working with Data. I find that "odd".
I assumed it was a software issue not a hardware one given the emotion chip isn't giving him skin or endorphins, but presumably simulating emotions in a positronic brain.
I would say it could have been a software issue as well. Or there might be some minor changes in design so that Lore and Data are 99.9% identical in design and construction.
It's hard to believe that Lore needed an emotions chip. He always seemed much more emotional than Data, even in his first appearance. I wouldn't be surprised if Data's emotion chip combined with Lore's proto-emotions would lead to a crazier Lore. And what do you know - it did. In his next appearance, he turned Data into an addict and turned a bunch of loose Borg into a cult.
It would make sense that the chip was incompatible with Lore due to software issues because Lore already had emotions. By plugging Data's emotion upgrade into his own neural net, it made Lore go from psychopath to megalomaniac/psychopath. In essence, the programming glitches introduced by two sets of emotional subroutines gave him craziness along with his normal state of evil.
A slight difference in programming that created a maniac vs a well adjusted being I too echo the sentiment that Lore's programming was simply not designed to additionally have Data's emotion chip programming together. Obviously the tech was compatible. Data & Lore are compatible with almost all the tech we ever see on the show. Riker hooks his head up to the warp core in Disaster, for god sake The concern was that Lore was not programmed to have Data's emotion programming. He already had some kind of oversight in his own, that Soong never got around to fixing, because he thought him inactive. Sadly, I suspect he could have helped Lore, but the result of combining the emotion programs was that he murdered Soong, which seemed even too much malice for Lore himself earlier in the episode when he showed distress at the idea of Soong dying. I always felt the original problem with Lore was that he was made "Too Good". He had better strength than a person, & better intelligence, & at least the way I see it in Spiner's performance, his emotions are stronger than a Human's too. He is carried away by them. Thus why he can be mad a Soong one minute & then in a flash, be distressed to find out Soong is dying. He's overly emotional on a dangerous scale This is why I don't hate "Descent" as much as most people, because even though it might be a paltry development for the Borg, it was a fairly crafty evolution of Lore, post-emotion chip. It turned him from just a overly emotional genius into a ruthless megalomaniac, hellbent on ruling the Galaxy, & with Data under his control, I believe he could have succeeded
Also in Time's Arrow they could tell it wasn't Lore because Data had an 'L type brain'. I think the problem with Lore is that Soong tried to program more realistic emotional behavior.
Lore was on Vista with it's compatibility issues, Data on the more stable Win7 and B4 definitely on the trainwreck that was Me
Given we've seen how holograms can be created with perfect human emotions and ambitions (moriarty), it strikes me that its probably not difficult to "scan a human brain and make a duplicate of emotions." It's just that Soong's positronic brain/android body makes a figure more inclined to be like Khan or the Augments. Supermans rarely have humility or compassion. Data without emotions gave him time to adjust to ethics.