I customised both to the exact same degree so I am not sure what you mean. I am honestly not following.
Simply put, those components may not have the same costs associated with them. If your mental model is that Dell just puts all the parts that go into their machines into one big pile and then just selects parts as people fill out the webform then that's the flaw.
Here is a simple example can see after a couple of trips to the local store. First stop is cross town, moderate distance trip to a "big warehouse store". There you buy a big 48 roll package of toilet paper. Let's say you pay $0.50/roll for that.
Sometime later after you have put the last of that 48 into the dispenser in the upstairs bathroom, unexpectedly a large group comes over to for a party/watch sports/whatever. Large group in the house and no more toilet paper. Oh snap. So you run a much closer store and buy a package of 4 at $0.60/roll.
A short time later the downstairs bathroom runs out and you put one of the new rolls on. So you have a $0.50 roll upstairs and a $0.60 roll downstairs. "Unfair pricing"? Not really.
It actually should be more surprising that it is not optimal to first pick the starting point
closest to the final result you want to get the best price. What you are saying is that customers should pick the configuration that is
furthest away from what they want, spend
more time configuring it, but still end up at the same point. The loopy-ness starts right there at picking the furthest distance to start from. That makes sense????
Picking the closest configuration means that Dell has the highest probability of having pre-ordered in bulk most of the parts you are about the buy. By selecting the configuration furthest away means you are
lowering the probability to the smallest amount possible that Dell has pre-ordered in bulk the parts you are about the buy.
So you may end up exposing the "bulk buy" parts costs versus the "spot market" (or "low volume") price.
The vast majority of people actually follow the rational strategy of selecting the computer
closest to what they want as a starting point. Dell would be loopy to bulk order large amounts of parts that only single digit percentage (or less) typically add to a starting configuration. They bulk order what expect people to buy (i.e., the parts in the typical configurations) in the quantities those models are characteristically are ordered in. That will lead to a system that leaves minimal inventory at the end of the week/month/quarter.
The fact is they aren't the "same" machine when finished. To the inventory tracking system one is likely the "SKU model 1234 with 23 mods" and the other is "SKU model 1235 with 10 mods" .
What is dubious is for those 'config to excess' options to be in the system in the first place. If people can only configure a "entry" model up to a "base" model then if they are looking for something larger/bigger than base then would back out and pick a better starting point and get the better price by themselves. Likewise, if the base is "too big" then pick another config one step down. Dell's SNAFU system is that there 20 different ways to wander through the maze to get to what is superficially the same place.
So users who pick an configuration option that is only rarely selected the pricing can change. This is because the parts come out of different "buckets".
P.S. One likely reason that the phone operators can get better pricing is because they are familiar with the byzantine model selection and do the task of picking the "closest starting point" better than users confronted with a half dozen grossly (if not gratuitously ) overlapping ones.