Thanks all for the answer.
The enblend -l1 is definitely the solution and works pretty well, it gives 
more gap but at least the temperature are consistent.
Nano doesn't change the value apparently but because the pixels shapes 
change the value appears different on my software but that's not an issue.
So I think I'm good.
So here we see that it's possible to work with FLIR thermal imagery without 
purchasing their ultra expensive stitching software which is a good news!
Thanks a lot for your help

So for summary of this discussion and to help people who would like to do 
the same here is the options that has been selected :

For the PTO

# hugin project file
#hugin_ptoversion 2
p f0 w20000 h29579 v54  E0 R1 S6623,10647,615,28015 n"TIFF_m c:LZW r:CROP"
m g1 i0 f0 m2 p0.00784314
# image lines
#-hugin  cropFactor=1
i w640 h480 f0 v1.98299759399113 Ra0 Rb0 Rc0 Rd0 Re0 Eev0 Er1 Eb1 
r27.8521414389429 p-32.3543915502492 y-5.94771868772334 TrX0 TrY0 TrZ0 j0 
a0 b0 c0 d0 e0 g0 t0 Va1 Vb0 Vc0 Vd0 Vx0 Vy0  Vm5 Rt1 n"Rec-000842_50.tif"
....

# control points
c n0 N1 x68.1716594051952 y61.2351178588815 X96.5287897418657 
Y225.914218938934 t0
....
#hugin_optimizeReferenceImage 0
#hugin_blender enblend
#hugin_remapper nona
#hugin_enblendOptions 
#hugin_enfuseOptions 
#hugin_hdrmergeOptions -m avg -c -c
#hugin_outputLDRBlended false
#hugin_outputLDRLayers false
#hugin_outputLDRExposureRemapped false
#hugin_outputLDRExposureLayers false
#hugin_outputLDRExposureBlended false
#hugin_outputLDRStacks false
#hugin_outputLDRExposureLayersFused false
#hugin_outputHDRBlended true
#hugin_outputHDRLayers true
#hugin_outputHDRStacks false
#hugin_outputLayersCompression LZW
#hugin_outputImageType tif
#hugin_outputImageTypeCompression LZW
#hugin_outputJPEGQuality 90
#hugin_outputImageTypeHDR tif
#hugin_outputImageTypeHDRCompression LZW

i created that in the Hugin GUI

Then I created a bat file with 
"c:\hugin\bin\nona.exe" -m TIFF_m -o 824 824.pto
"c:\hugin\bin\enblend.exe" -l 1 -o pano824.tif 8240000.tif 8240001.tif ...


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