This was done on a Prusa I3MK3 without multi material.
I first printed the logo which is only 1 layer thick, then I printed the case over it.
To do this I loaded the case into Slic3r and added the logo as parts, I selected the case and applied 0 to infill, perimeters, top and bottom layers. This way it will not print the case but only the logo in its correct place.
Once the log is printed I did not remove it, just the skirt and purge line.
After I reversed the parameters, logo has 0 everything and case has the default settings again.
And print the case on top of the logo that is already there.
Since it is only 1 layer thick the bed leveling does not touch the parts already on the bed and it prints it on top without issue.
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