The 2000+commlink cost formula is just there to tell you how much the base cost of the implant. The implant version of a commlink has base cost of 2000 nyuen more than the non-implant version of a commlink. That formula doesn't create a difference between how commlink implant grades work as opposed to all other cyberware, it just reflects that there are many different models of commlink which each have their own cyberware implant version. Nowhere in the text description of the commlink does it say you paying for two separate things "an implant and a normal commlink". In fact, its text is basically identical Vision Enhancement.
Commlink: An implanted version of the commlink (p. 327), popular with hackers and salarymen on the go. A Sim Module (modified for hot sim or not) may be implanted at additional cost.
Vision Enhancement: An implanted version of vision enhancement (p. 333).
If it were meant to work differently, it could easily say so. In fact, the core book even goes further and notes that accessories of cyberware implants must be purchased at the same grade as the implant they are attached to. So even if you did somehow believe that you were dealing with an implant and a normal commlink attached to it, the commlink would still be affected by grade cost modification, RAW. Moreover, the ACTUAL examples of in the Augmentation book include alpha and betaware version of the Caliban Fairsight commlink. Do the math, the TOTAL cost of the commlink is clearly augmented by cyberware grade in all the examples.
This has nothing to do with a desire to gyp players out of resource points, its just how the rules are actually written. My personal opinion as a player and as a somewhat permissive GM would want them to be cheaper too, but I'm just trying to be objective here and answer the "what is" question rather give my opinion of the "what ought to be" question. There is absolutely no evidence anywhere indicating that a commlink implant is somehow special and that part of its cost isn't affected by grade. Not that such an argument is entirely convincing either way. All cyberware versions of things basically cost more then their non-cyberware counterparts and choosing to make them alphaware makes that even more true. There is no reason to view commlinks as an exception to that or to say that treating them the same as every other piece of tech with a cyberware counterpart is an attempt to gyp players out of resource points. Vision Enhancement, again for example cost 300 nyuen for rating 3 non-cyberware, 4,500 nyuen for cyberware version at the same rating, and 9000 for alphaware cyberware at the same rating. An alphaware cyberware version of the same tech cost x30 (that's 8,700 nyuen more) as much as the base non-cyberware tech. So why on Earth would an alphaware cyberware version of a commlink only cost 4,000 nyuen more (undoubtedly a mere fraction of the overall commlink cost)?