The immobilizer issues are common with the New Beetle; these threads might be helpful:
immobilizer problem
http://newbeetle.org/forums/1-8-liter-turbo/61381-immobilizer-problem.html
Stalling After Start Up
http://newbeetle.org/forums/1-8-liter-turbo/61375-stalling-after-start-up.html
The most common problem; is the wiring to the "reader coil" is damaged and has intermittent connectivity problems; sometimes, the reader coil is bad or the immobilizer that resides in the speedo cluster is faulty. Every part of the immobilizer system; has to work together for it to work correctly. This system is made up of: the key fobs with internal immobilizer chip, the reader coil that reads the rfid chip in the key fob, and the immobilizer that reside in the speedo cluster and the ecm that runs the whole car.
To begin with; on a very basic level, I would get the car scanned and see what trouble codes come up; some of the codes can be very specific and tell you what in the immobilizer system has failed. This isn't always the case but it is a good foundation from which to start from. The dealer; is giving you incorrect information, the system can be repaired and parts are available to do so; frankly, I do not understand why that are not taking steps to repair the problem, unless you decided to not go ahead with the repair process.
There are companies; that offer speedo cluster repair; so, if the immobilizer/speedo cluster is faulty, it is possible they could be repaired or just replaced by buying a used one or a new one from your local Volkswagen dealership.
Here is a good page; that breaks the immobilizer system down for you:
VW immobilizer technical information and problem troubleshooting
disable immobilizer solutions:
There are a number of companies; that will modify your ecm to eliminate the immobilizer in the software that runs the car. The other option; are Chinese knock off plug in immobilizer delete tools; that offer the ability to turn off the immobilizer through the software in the ecm, by just plugging in the tool and it does it automatically.
I have not tried; either solution but I am in the process of repairing and fixing my immobilizer problem. I am going to start with replacing the wiring to the reader coil plug; if that doesn't work, the reader coil/key tumbler and if that doesn't work, then the immobilzer/speedo cluster itself.
Vag Immo Bypass Device,EDC15,EDC16,ME7
This is the chinese made plug in tool that defeats the immobilizer in the ecm; there are a number of different models out there, I have no experience with any of them. It is tempting to try this type of solution.
https://www.google.com/search?q=vol...izer+bypass+tool&sa=X&spell=1&ved=0CCsQvwUoAA
Immobilizer bypass through ecm software modification:
It seems a number of companies; that offer this software delete modification, Revo, APR and others offer this option on their respective websites.
https://www.google.com/search?q=vol...&psj=1&q=volkswagen+immobilizer+defeat+coding
I am of the approach; I want to finally fix this problem and have the immobilizer/security system feature intact as the factory intended. I appreciate, you desire to eliminate the immobilizer and thus just not have to worry about fixing the problem; I like to fix thing and I am going to!
I hope the above info; helps you in your search for a solution, to your immobilzer problem.