Tesla Model S at company's Fremont factory
Tesla's updated Design Studio packages vehicles into three simple categories (trims): standard, premium and performance.
We already know that there will be less than 100 different configurations for the upcoming Model 3, and also that there will be few battery options (at least initially), and likely a very simplified Design Studio. Tesla just updated its configurator (if your browser can manage to not redirect to the old site before June 8th) for the Model S and X, and it may be a sign of what lies ahead for the Model 3.
Tesla Model X
The new configurator gives you the choice between 75 and 100 kWh battery packs, since the 90 kWh pack will be phased out/not offered starting on June 8.
Tesla refers to the 75 (no all-wheel drive) as the "standard" model. The 100D is considered the "premium" trim, with the P100D being the "performance" model. Now, vehicles won't be classified so much by battery size, as they will by trim, more like traditional automakers.
As Tesla moves forward toward mass production of the Tesla Model 3, it has had to consider the advantages of simplicity. Having less unique configurations assures that the line can move more quickly and efficiently, which lowers cost.
No need to overthink it or worry, however. At this point, and likely into the future, customers can still add options and extras, and stray from the three primary trims. Let's not forget that Tesla just released a chart comparing the Model S to the Model 3, and touted the Model S' 1500+ configurations.
You can choose a "custom-built" option, which redirects you to the old configurator, if the standard options don't suffice. One example would be if you wanted a 75D. It wouldn't be any different than ordering a vehicle from GM or Ford, and selecting the all-wheel drive option. This would also be true for those seeking a 90, until that battery pack goes away.
Another option is to simply select one of the standard choices, if most of the build suits your needs, and then add available options.