Exactly. The BTO options are basically zeroed out for the trade in. If you're someone who plans to upgrade their machine frequently using the trade-in, go with one of the primary configurations.
One of the issues is also that there's usually no good way to search for exact configurations when looking for traded in machines. Meaning that it's harder to convey the value to the end customer.
The search seems like an easy problem to solve. A set of options to select when you offer up a machine for trade is viable for any self built system. For Apple, they could just link your original purchase data so could be even easier.