Reflects more about what the different groups pricing levels are to them at OEM.
This is another example of a consumer thought process behavior that always seems to make sense to the consume but leaves the retailer scratching their head.
The short of it: If you want it, buy it. If you don't then don't. I think you'll find inventory and availability issues more with the Di2 options but let's say you don't and you feel you can get the mechanical then buy the Di2 aftermarket and save overall then go for it. It works for you. It works for them. They still sold you a bike.
What it isn't - it's not a window into some sort of nefarious scheme whereby Trek was planning on flossing every customer ever and now you've spoiled it and exposed them for the outrageous corporate drones they are.
Long Examples and discussion:
Pricing. I have written a lot in this forum over the years pertaining to pricing models. One of the worst problems with US retail or businesses in general is that many take the old "cost plus" model of pricing. This is the model that most consumers actually believe is the basis of establishing a retail price. It isn't always and honestly should never be. Prices should be set at the level customers see value at in the market. That natural sweet spot of price to units sold that we all remember from the "guns and butter" graphs in basic Econ. Those models never talked "cost". The reality is if the value in the market for a product is $5 and at that price the seller is selling the amount of units/volume they desire then that's what the price should be. If it costs them $5.01 to manufacture the product then they have a problem. If it costs them $1 then they have a seemingly good position. That's the basics.
Problems with market pricing: when it's taken advantage of in markets with need based in human survival that can't be satisfied through competition. Food, medication, etc. but meh - not my discussion and this is bike parts.
Reality though is that most arrive at their pricing models through a combination of cost plus and market pricing. Example from my business: let's say I have a wheelset and the cost side is such that when I put the margin on it that I need to get in order to survive it results in a weird number - $1404. Market pricing would push me towards making that price $1399. At the same time if it's sitting at $1362..... $1399 looks better and consumer behavior is such that it will be interpreted as the same price to most. Sometimes you win sometimes you lose.
Right now a couple of armchair economists who are actually engineers are pulling their hair out at the idea that pricing isn't simply a set equation for every situation.
What really goes wrong with the situation I described in the last example is that there isn't that incremental "component parity" that was the cause of the initial post. What I mean is that while it is easy to see in the one situation how I could easily round the price to $1399 because it looks better, has a proven psychological effect on shoppers, maximizes market value, etc. it could cause the "component upgrade price" of let's say the hubs to not match at this level in the same way they would at a price point that is roughly half.
Try at an example: Option 1 with brand X component = $1199. Option 2 with brand Y is $1399. Incremental component upgrade cost is $200.
Now let's change something major about the configuration of the product. If it was wheels let's go from carbon to alloy rims. If it's bikes then from a carbon to an alloy frame as an example.
Option 3 with brand X components = $649. Option 4 with Brand Y is $749. Now in this example the incremental component upgrade cost is $100. Same component difference as above. What's changes is the underlying cost structure of the package has roughly halved. Half your cost structure but apply the same markup % to get the same margin % after the sale and you will see this happen. It can be a royal PITA to keep parity in these upgrade pricing differentials AND preserve final pricing structure. Damn near full time job.
In order to preserve parity you have to either undercharge for the upgrade at the high level frame/rim or overcharge for the same upgrade at the lower price point configuration. You have to let your customers and the market be your guide.
In the original post - I am sure its a difference in cost structure for the component upgrade that bears no direct relation to what you are seeing as the retail price for the group through outlets selling off of MSRP. There are so many factors at play when setting pricing on an assembly that the retail price through internet brokers of some of the component parts aftermarket after you've already had the bike on the market is meaningless.
As a result some of this pricing disparity can happen and seem weird to those on the outside.