You need to consider how the math pans out. For the Model Y, there are 3 different trim levels, 5 different paint colors, 2 different wheels (for non-performance), 2 different interior colors, and 2 different hitch options (yes or no). That alone makes for 2 x 5 x 2 x 2 x 2 = 80 different non-performance combinations, and 5 x 2 x 2 = 20 performance combinations, for a total of 100 unique build configurations. Adding another binary option (e.g. Homelink) would increase it to 200 unique build configurations.
The more build configurations there are, the less likely it is that a build configuration can be found to match your order. That increases the likelihood that your car has to be custom built on the assembly line, meaning a longer wait for your car. It also makes it increasingly likely Tesla might have trouble finding someone to match up your custom configuration to someone else if you back out of your deal, meaning they have to store the car somewhere.
For an option that has to be built as you want it in the factory, there is no other option but to have it set up that way in the factory. But for something that can be easily added later, it makes much more sense to add it after delivery.
Some of this stuff will become easier once Tesla delivery infrastructure grows to be able to handle their volume. But for now, their infrastructure is lagging behind their growth and probably will for the foreseeable future (at least another 3 years, considering the Cybertruck).
