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This is probably a non-issue for most LW users today.
If I recall correctly, the problem I'm describing has to do LightWave Joints and how the weight map assignment is offset to the previous bone compared to other programs like Maya and MB, making the FBX file less compatible. What this means is, after importing an FBX from another program, you were required to manually reassign the weight maps to the correct bones for LightWave. But when you import only the motion envelopes, the offset weight map was not a problem because the hierarchy/names in the rig remained consistent.
The frustrating thing about this issue was that, during beta testing (way back in LW 9.6 - LW 10 days,) the weight map assignments for Joints matched the rig in Maya and MB assignments by default. I still don't understand why they changed that for the final release.
But...if you're using Bones, this shouldn't be a problem, so I would stick with that. Sadly, there are a lot of nice advantages when editing rigs using Joints in LightWave, but I pretty much abandoned them for Bones at this point.
That said, I still think it's better to use two different rigs, one for final shading in LightWave and one optimized for quick previews and interactivity in other programs. So long as they share the same rig, importing only the motions from the FBX is all you need to do.
(FYI, this is still an issue for the 'Brudders' project which I'm still working on. The rigs used in this project were set up using Joints, and it is just too much trouble to change that now.)
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