This is a known issue since BW7.0 until BW7.3.
The reason (I believe, though SAP may want to correct me on this), is because in certain cases due to different logical system mappings, the TRFN objects being imported has to be re-created and regenerated in the system,
e.g., you create a TRFN in DEV, it is linked from ECC-DEV > BW-DEV.
When you import this TRFN object to your QAS system, the logical system mappings must change to ECC-QAS > BW-QAS. This results in a completely new TRFN object being generated (with a different technical ID that is different from the one you saw in DEV.
This is the reason why you see the IDs as different in each system. The only linkage in this case is as you correctly pointed out can be found in field RSTRAN-ORGTRANID.
In the transformation rule details, you can also view this original transformation ID by going to the menu "Extras" > "Object Directory Entry". The original transformation ID from DEV will be found in this popup menu.
I know this may be a little disorientating especially if you're trying to trace the TRFN objects across the landscape, but unfortunately there is no better alternative (in keeping the technical IDs the same) for the reasons as explained above.
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Going by the above behavior, this means that the issue with different transformation IDs being generated should happen only with transformations that come from DataSources only, and not transformations linking two InfoProviders together (check and see if this is the case in your system!).
However in certain cases, I have noticed that there are different technical IDs generated for transformations from/to 2 InfoProviders (e.g., DSO to InfoCube). This usually should not happen, but even if it does, there should be no issues with the data loading. The reason I found (though SAP may want to correct me again on this), is because certain TRFN objects were activated directly in QAS/PRD.