Provided you have a 5 port junction box, you absolutely can. Pretty much as simple as making sure the firmware plays nicely and then its plug and play.

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Benjamin Deal - Professional - Instagram - TriRig - Lodi Cyclery
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Certainly can.

Best of both worlds and one of the best reason to go Di2. Just need the 5 port junction (since you'll be adding 2 more cables) and the TT controllers. Just plugged them in and I was good to go.

You bet it works, and it works pretty darn well.
Here is an example from this guy (some oddball named, 'DeBoom' ) who did it on his slightly unusual (but effing fast) tri bike:

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Awesome to see this- hopefully adding a junction box in the frame compartment of the Madone is easy enough. Looking forward to giving this a go! Will it the extensions fit in the end of all profile design bars?

I believe so, most aerobar extensions (including those from profile design) are 22.2mm (7/8") in diameter, and di2 endshifters are made to fit those ...

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So if I I have the 2019 Madone it has a 4 port I believe. I haven’t pulled it out but looking at the manual - are all four used (front d, reared, shifters, battery) or do the ports refer to shifters only? I ask because if I had one pot open I’d consider just Running a rear shift control to the bars as imagine in tris not shifting too much in the front. The other issue is I’m not sure there is an internal 5 port.

if you have one port available, just get a 4 port hub (sm-jc41) and short extension cable and daisy chain them

So look a bit further through the Madone Assembly manual (pages 21 & 22 - some more schematic info shown in front on page 3) and the Di2 configuration for the handlebars and stem is shown.

The JC41 4 port Junction B in the downtube has all ports in use for RD, FD, Battery and link to bars. Trek is using the y-splitter e-tube harness in the bars to link the Brifters and right bar end RS-910 2 port Junction A to the line from the downtube Junction B. To make that link they are using the inline JC200 2 port e-tube Junction B.

So you would probably want to make your link at the 2 port Junction B. You could use the 4 Port JC41 here (you won't be using the 5 port Junction A unless you want to ditch the handy bar end Junction A controller/charger port set up - only one Junction A allowed per system).

Depending on the handlebars and wiring access that comes with the Madone bars a more elegant set up might be running e-tube wires to each of the 2nd ports available on the Ultegra brifters. Then you could either link these or use a single JC200 2 port Junction B per wire. I think the best set up will be dictated by how often you want to swap out the aero extensions. If there are holes in the bars near the stem (due to the aero routing I think there are cable exits here) you could leave the e-tubes right in the bars and only link them when you bolt on the aero extensions.

Trek's manual is pretty cool as the back pages list out Di2 wire lengths for different size frames and bars.

Wow, this is super helpful, thanks for spelling this out. The way I read the schematic, I came to the same conclusion regarding all four ports being used but wasn’t clear on how it worked up front, I’m not a very mechanically minded racer (trying to get better). The way you spelled out having the open connector ports where the wires exit the stem is definitely what I’m looking for as I want to be able to take the clip ons on and off relatively easily. Figure if the connector is there I can connect it w the other wires when not in use and will more or less be hidden. I’m going to need to read a little more closely how you describe this, and probably enlist a mechanic, in the worst timing ever my shop and mechanics of 5 years just closed. First 70.3 in a little over a month I want to get this dialed in for. Will take some time to better research this weekend, thanks again for spelling this out!

For those who have done this. I'm curious, what % of time do you keep the clip on bars mounted?