Below is how it worked with the Model X and from everything I have read this is how it will work with the Model 3. Elon Musk DID say that higher optioned cars would be produced first. This was during an interview right after the LA unveiling of the car. I went back and listened to the interviews to make sure. Also, Elon said that those who already owned a Tesla would be put to the top of the West coast group but after the employees group.
Those who put down a $5k deposit for a Model X were given a reservation number (RN) and a reservation sequence number (RSN). The RN was just a customer identification number. The RSN was a sequence number which determined the order in which a person would be allowed to access the design center. I had reserved about six months after the first reservations were taken and therefore my number was around 8,000.
Starting the last week of November through the end of December they opened up the design studio. Those with the lowest RSN were invited to configure first and those with the highest numbers were last. By the end of December all of those waiting to configure had been sent invitations. Starting in January you could go directly to the design studio and place your order without being invited.
With a RSN of around 8,000 I was invited to design my Model X on December 10th. I configured my Model X and placed my order the day I received my invitation. Because of this I ended up going from 8,000 in line to having my car made in the first few days of production, the second week of January. Cars are not necessarily produced in VIN for many reasons. After they made the first 100-150 cars around the third week of January they shut down production for three to four weeks to resolve the many issues they were having. By the time they started making cars they had 5-6k worth of orders in queue and queued (ordered) them based on certain criteria. Those who ordered the Model P90D with both the premium and autopilot option packaged were produced first. Even though I ordered ludicrous mode it wasn't one of the options which moved you to the top. My car came to $155k. Those who didn't order the Performance edition (P), who ordered the smaller battery and who didn't order the premium option and autopilot options were produced last.
What I learned from this experience and what will most likely apply to ordering the Model 3 is:
You will be allowed to configure based on the following order: Employees, Current Owners, West Coast, Center of Country, East Coast, other counties.
When you are invited to configure it is important you configure and place your order the day you get the invitation. Waiting a few days to think about the options and what you want could delay your delivery by many months.
What you order will also impact when you get the cars. Even those who disagree Elon, specifically indicated the week the car was unveiled that the more optioned car would be produced first. One of the main reasons for this is they group like cars together during production. Producing like cars together helps speed production. From a profit standpoint it makes financial sense to produce cars with a higher profit first.
There has been a lot of discussion when production will start. Officially, they said Model X production started in November 2015 but in reality only 7 Founders cars had been made and these cars were made by hand so they could say that production started during the second quarter of 15. In reality production for signature cars starts in late December and the true production cars started in January/February.
From everything I have read by professionals who follow this in the industry indicate Model 3 production will probably not start until late 2017 with full ramp not until mid-2018.