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if you are using shells defined by surfaces or based on faces, no need to change the 3d model thickness
if you are using sheetmetal, you need to change the 3d model because the sheetmetal shell inherits the thickness of the 3d model
there are 2 caveats
1. in the long run, you'll have to change the 3d geometry so that you have something for manufacturing. so changing it at the 3d model level could make sense before then updating/changing the shell.
2. remember that shells assumes you are choosing the center of the part (mid plane). usually we don't do this and have to account for this either with an assumption (that the part is thin enough that choosing inside or outside face doesn't matter) or by adjusting using the offset. so they may be suggesting changing the model for this.
Thanks a lot for your insight.
Have a great day ahead!!!