I'll just make the observation that the muscle groups I use do change if I go into a more Aero position.
( Either for hiding from the wind, or for TT. )
In 'normal' riding, it's my quads that do most of the work, and after a long 'normal' position ride, I mostly feel it in my quads.
I became aware of this when I started TTing, and once down in areo position, I was engaging my glutes much more, and my quads much less.
At the end of a long TT, is't always my glutes that are really feeling it.
So it could just be that as you changed position, you began to engage muscles that were much less accustomed to being put under that kind of strain, and so they are protesting a bit.
Could you compensate for that by changing seat height? Possibly. In might have the effect of returning your body position to one which is closer to the one you are accustomed to.
Personally, when preparing for the 24h, I just rode a lot more 'in position' to train the other muscle groups to get used to it.