With conditional pricing, each brand or SKU (if you made price conditional on another attribute such as brand or SKU) has a different set of prices.
For computing WTP, we strongly advise to use the competitive simulation approach rather than estimating the algebraic approach. When using conditional pricing, this is even more a concern.
The competitive simulation approach involves putting a test product (for which WTP will be estimated) into the market simulator in competition with a large set of realistic competitive products. Perhaps that's 8 or 10 products, plus an additional "product" in the None alternative.
Let's imagine you want to estimate the WTP for "has sunroof" versus "doesn't have sunroof". You first specify your product (the product for which WTP will be estimated) in competition with the realistic set of competitors as would be seen in the marketplace where your product does not have a sunroof. Write down the share of preference for the test product (perhaps it is 12%).
Next, change the test product to have a sunroof. Keep the competition constant. Run the simulation and write down the share of preference, perhaps it is now 15%.
Next, increase the price for the test product with the sunroof until its share is driven back down to 12%. That difference in price that leads to indifference in share of preference for having or not having a sunroof is the estimated WTP for sunroof.
This approach takes into account the conditional pricing table, as the market simulator knows how to map actual prices to the conditional pricing table for simulating share of preference for products.