Thanks for the tip. What I ended up doing was :

- export individual panorama stacks at their respective exposure
- export them after matching the exposure of each stack to the other stack's 
exposure. This means I ended up with as many panoramas as the number of stacks 
squared (^2). I did this by right-clicking in the photo list, then selecting 
"Manipulate image variables" and entering a formula like Eev=val-2 (or +2)
- in Gimp, import everything and group by exposure level (so each "exposure" 
group contains all the stacks with matching exposure)
- mask in the parts I want so that all the tree branches are fixed accross all 
groups
- export each exposure group
- import them in a new Hugin project
- Export the fused panorama

I noticed some limitations with that technique that might have a solution (not 
found yet) :

- At first I tried manipulating the exposure variable on an imported single 
panoramic image (previously exported from Hugin) instead of manipulating the 
original pto with the individual photos but this did not give the same colors. 
This meant I had to manipulate the exposure on the original pto for exporting 
the "matched exposure" panoramas. This wouldn't be a problem if blending was 
deterministic but since it's not, the same stack at different matched exposures 
was not consistent in the blended parts, since branches move between individual 
photos.
- As you'd expect, matching the exposure doesn't produce an identical result as 
the exposure you matched. For example the blue sky may be blown out in a high 
exposure photo, so if you bring it down to match a lower exposure where the sky 
is blue, you'll end up with a grey sky. This was totally expected. However, I 
did not expect some other color differences, like the over-saturation of green 
leaves or the slight difference in contrast in some areas. Not sure if this can 
be solved, though it wasn't too noticeable in the end result.

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