You have an issue that is caused by the underlying operating system and the communications protocol it uses to talk to the EBCM, it is not a matter of having the wrong values in the little editable, visible boxes and if you could just find the right numbers to put in the little boxes everything would work yay!
2006 H3 3.5L and 2008 H3 5.3L use the exact same EBCM (25939761). It is a completely different design/family/architecture than the 2008 TBSS EBCM (20817362/20817363). They speak different languages. Which EBCM language the E67 speaks is determined by what operating system it is programmed with.
What you need to do:
Get your ECM flashed at a dealer, or by someone with tools that can flash using GM SPS, using a real VIN from a 2008 H3. (5GTEN13L488105438)
Connect with HPT, read&save the file from the newly-programmed ECM
Open the new '08 H3 file, click 'Open Compare File', load the old TBSS file
Click Compare, then View Comparison Log
screenshot.20-01-2021 01.04.15.png
'Copy All Differences' will copy EVERYTHING that is different. 'Copy Selected Differences' will only copy the stuff in the thing you right-clicked on. There are some things that will not copy over directly and will require hand-tweaking; for instance the IAT axis is different between the two files, but the values in the cells is the same - this will require finding tables like that and copying the axis from the compare file into the working file.
You cannot use the segment swapper between files with different operating systems, that's not what you need here anyway.