Slam the base bar and the pads should be at whatever height gets you to your fit coordinates. The idea being that the spacers for the extensions are more aero than stem spacers. Since you should be spending most of your time in aero, the base bar height doesn't matter to much (to a certain extent).

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Strava

the above advice is probably the most aero and popular solution--certainly it looks the best! It obviously depending how high you are talking, but, personally, I don't like slamming if it leads to the need to add a huge amount of bar spacers for a couple reasons: (1) reaching for brakes when necessary is more difficult; and (2) in training, with cars are around, lights/stop signs etc., I find myself on the basebar more frequently than I would like and a large drop is likewise not very comfortable. For me, I prefer to find a fit with 0-20mm of stem spacers and a max of ~30mm of bar spacers

The base bar and pads should be put in the best position for your fit; the gap between them is an output, not an input.

For the base bar, aim to recreate the hoods position. You only use this for climbing/braking/cornering, so being comfortable and having control are more important than being super aero (that’s what the aero bars are for).

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ECMGN Therapy Silicon Valley:
Depression, Neurocognitive problems, Dementias (Testing and Evaluation), Trauma and PTSD, Traumatic Brain Injury (TBI)

Just putting my first TT bike together. interesting to put base bar at hood height, was thinking drops. just waiting for a few bits before trying to get an initial position sorted.
A proper bike fit might be tricky this winter

A lot of cyclists set the base bar up as a drops position. IME this harkens back to the pre-aerobar days when the base bar was as low as possible to get aero (see Roche below).



Looking at what the basebar will be used for (vs. the extensions), hoods seems to make a lot more sense (especially if the course has significant climbing). Even more so given that you need to be able to run off the bike, and that 70.3+ races have bike legs that are significantly longer than TdF TTs.

Here's Frodo. His base bar setup produces a more upright position than the aerobars; more akin to hoods.

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ECMGN Therapy Silicon Valley:
Depression, Neurocognitive problems, Dementias (Testing and Evaluation), Trauma and PTSD, Traumatic Brain Injury (TBI)

makes sense and the point about training and being able to get to the brakes easily seems valid.

impatiently waiting for a bottom bracket so I can get my cranks on and get a feel for the bike.