Aliases are created the way they are to "transparently" (sic) refer to the main part. If a tool author decides to "warn" the user about a singular reference, I believe the usability issue lies with the tool, not the library. Why does MLCad even care? How does it know - from the LDRAW_ORG line, or because the file contains just one type 1 line?
Chris (LDraw Parts Library Admin)