If done correctly and you follow "the rules" and pay attention to "the fixes," the install should be fairly clean. I personally had Car Toys do the installation, and I would suggest a professional install if you are even a little shaky about tearing the car up (even though this will likely add a good chunk of change to the purchase). The system is an excellent system and regardless of the term BETA, the customer support is still excellent. If you compare to the free software and cheaper hardware out there, this is still a more complete system.
The difference with Streetdeck is in the quality of workmanship on the software package. I have tried a few others and can tell you that even though they offer similar products, but there is no support and things don't always work as you would expect from those packages.
If MP3CAR is willing to continue to support those of us that spent the money to put their system in our cars and give us the opportunity to receive the software upgrades for free (and if hardware, then discounted), then I think it makes no difference. What I would do is list the hardware you intend to buy and ask for a suggestion on the install of that hardware. This should get you a good idea of the issues people have had and save you a lot of heartache...
The bottom line is that Streetdeck is not for the weak pocketbook, but is definitely an extraordinary system (even in BETA).