Processor Limit isn't based on the stats, but something you pick when designing the Nexus. The price then depends on how much extra space you want.
For example, if you want a filing system supporting only half a dozen people and 1 program each, you'd go low in the Processor Limit, sticking to 12. If you want to support a dozen people+ics using on average near-3 programs, you'd want to go for the maximum of 50.
You say the Persona Limit of the example nodes does not follow the first two rules. The first list of examples, however, does follow the Persona Limit: Each sample Nexus on p50 has Persona Limit as Systemx3. The Processor Limit, however, depends on the Nexus's owner's choice. Only the prepackaged Nexi aren't exactly equal, which may be a miscommunication or simply representing how corps can get things done differently.
So the small matrix cafe doesn't care about programs, whereas the online shop wants people to run Browse and thus has a higher Processor Limit. The Large Matrix Cafe knows some people will use programs, while the Public Library knows people will be employing programs to help them find and do things.
Each individual persona is limited to their own Systemx2, not the Nexus itself. The subscriptions of the persona aren't relevant, only their subscription to the Nexus matters and that's the Persona Limit.
Let's say I want a Nexus. I want it on System 4, which means the Persona Limit is 12. I want a Firewall of 6 and a Response of 5, and a Processor Limit of 20.
The Response has an availability of Response Rating x 4, so 20. It costs Rating = 5 x Processor Limit = 20 x 100 nuyen, so 10.000 nuyen.
The System has availability Persona Limit / 2 = 6, and costs Rating = 4 x Persona Limit = 4x3 x 50, so costs me 2.400 nuyen.
And the Firewall of 6 has Availability Processor Limit/5 = an easy 4, while it costs Rating = 6 x Processor Limit = 20 x 50, so costs 6.000 nuyen. So this Nexus costs me 18.400 nuyen for System 4, Firewall 6, Response 3.
If I wanted a 50-PL R3S3F3 system, it'd cost me 11.925 versus the 10k of the Evo Mobile Terminus which has a better Persona Limit because Evo cheats. The MCT Sentinel is overpriced on the other hand.