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There are several possible reasons:

• The tool's origin is offset that much from the end of the physical part of the previous link due to some extension part, such as an attachment plate that effectively becomes part of the previous link by moving with that link, not with the tool.
• The STL file that is used to display link_6_t is slightly shorter than the real part.
• The offset in the URDF for the tool's origin is incorrect.

If you have access to the real robot, I suggest measuring the offset of the tool link's moving part and seeing if it matches the URDF file. If you don't, then try adding the URDF for a tool to the Motoman URDF and seeing if the moving part of the tool has its origin correctly aligned with the rest of the arm.