But that rule isn't present in the system. As such I cannot judge it under that adjustment, which is why I've been talking about the system as you represent it and noted it makes me feel extremely uncomfortable. And without that adjustment, the system gives munchkins plenty of space and you even said you'd allow it, but then you say you wouldn't allow it but it's not a problem because nobody at your table would do that. If it's only not a problem because nobody would abuse it, then it's still a problem because once someone wants to abuse what they can legally do, you're going to clash. It's better to design the system in such a way the situation cannot occur from the getgo.
The GM has a say, sure. But when the GM introduces a houserule that explicitly allows X, then when I want to do X he tells me it's not allowed, then the GM has made a mistake. We're not talking "I'm not letting you get X from the official books because I think it fits poorly with the campaign", we're talking "here, you can do X, no wait you can't bad player", and at that point the GM is an asshole and should have made the system in such a way that it wasn't possible to begin with. If you do not want 4/1/1/1 decks, you shouldn't give players a system that allows them to make it.
Anyway, your first post merely talks about completely custom decks. As such, I would not want to use your system since it leaves too much open. If you instead had an alternative system talking about customizing existing cyberdecks to increase them, then it'd be a system I'd like and it would be a system fitting with the tradition of upgrading your matrix gear within limits. Since this is a system about fully custom decks, I'm afraid I'm going to be skipping this houserule despite its interesting options and will just await Data Trails.