I think you could be talking about apples and oranges. It sounds like you may be speaking of a 2004 SRT and not the 2003's that went with the certificate program. Most (95%+) of the people got their price when they placed their order. The deal was that the person ordering the car controlled the ownership 100%. Unlike every other car deal out there (including the 2004 SRT), the certificate holder could go to any Dodge dealer (I assume they had to be 5-Star) and place his or her order and be assured they would get the car. You could literally shop your deal to every Dodge dealer in town and specify that you wanted the car for $*** over invoice. Didn't matter what the MSRP was (which absolutely NOBODY knew at the time), just that your price was based on factory invoice. That dealer didn't want to do it? No problem! Take your confirmed order to any other Dodge dealer you like - they were all competing for your presold car.
So, for most Vipers, your Dodge dealer might not have the allocation to get the car - or get it anytime soon. When I went to my local Dodge dealer in 1999 to order my GTS, they refused to go a penny below MSRP and then told me it could be 6-8 months to get the car. I posted something right here on the VCA message boards and got a reply from a few dealers, including Woodhouse in Nebraska. They had the experience (and allocation) to get my car quickly. They also gave me a heck of a deal. With the 2003 certificates, I could go to ANY Dodge dealer and they would get an immediate allocation for my Viper when they submitted my certificate. Because of that fact, many, many dealers offered to get the car for the certificate holder at invoice or slightly above. Indeed, another local dealer in Kansas City offered to get the SRT for $500 BELOW invoice. Why? Because they could not possibly get an SRT without the certificate holder bringing it in. It is a nice draw for them, even if it is only there for a day. Likewise, it may help them get future Viper allocations based on getting a car (or cars) in 2003. Also add the fact that they did not have to do any selling at all. The cars were aleady sold 100% and they were literally just taking orders.
For 2004, the dealers once again control the ordering process from start to finish and they will not be competing to get "presold" cars out the door. They will be "selling" Vipers once again and not just taking orders. They can order a Viper with or without you and have one on the showroom floor just waiting for that first person to plop down MSRP - or more. Afterall, in 2004 the SRT is available to the approximately 214,379,000 other adults in the United States that could not order a 2003. Just like the New Beetle, the Mini Cooper, and the PT Cruiser of old, the demand could very well exceed the supply and the dealers will control the price.
Bottom line: If you have a 2003 on order using a certificate, make sure you know what your price is. If they try to gouge you on it, you may be able to move it to a different dealership (don't know if it is too late or not). If you are talking about a 2004, do your best to stay at MSRP or slightly below. I don't think you will see many "+/- invoice" deals on them at all. Personally, I went with Woodhouse for my 2003 and am spending more for it there than many (probably most) people with a certificate. I knew that the follow up and the relationship was well worth those few extra pennies. I also expect them to buy me an apple pie with my Happy Meal this time...
Chris