I see what you are saying, CL-900 to CL-1600 = 701 numbers. The quote you gave is from Jay Miller's X-Planes book I think?
X-Planes 1983 Edition
Over a period of several years, a large number of design studies were generated by Johnson and his noteworthy engineering team. The various design designations included the series CL-900 up to at least CL-1600—some 700 studies in all!
X-Planes 1988 Edition
Clarence L. ‘‘Kelly’’ Johnson, during mid-1961, initiated an inhouse study effort to create a vastly improved, yet remarkably unchanged F-104.
[..]
Over a period of twenty-four months, some 700 design studies, assigned in-house Lockheed designators from CL-900 to CL-1600, were generated by Johnson and his famous ‘‘Skunk Works”’ engineering team. Numerous single- and twin-engine configurations were explored, with every one being
analyzed for its commonality with the F-104 and its relative performance improvements.
In his 1995 Lockheed Skunk Works book we have something quite different.
Over a period spanning some twenty-four months, numerous design studies, assigned Lockheed Temporary Design Designations CL-900 to CL-1200, were generated by the Skunk Works engineering team at Burbank. Numerous single- and twin-engine configurations were analyzed for their F-104 commonalty and relative performance merits.
As far as I can see, none of this is entirely correct.
from
mid 1961 we have CL-901, then there are several other "F-104 developments" in the CL-900 series. Within the Lockheed TDN system, generally alternate designs are numbered with suffixes. So, there were 21 known versions of CL-901 -1 up to -21.
The CL-1200 is first used in
mid 1969 for a VG Navy "VAM" study, but
29 December 1969 it is noted Lockheed Skunk Works division have taken this TDN for an advanced F-104 derivative and so the VAM work is continued under CL-1253.
The Skunk Works then uses CL-1400N (Navy CL-1200) and CL-1600 (LWF CL-1200) TDNs. CL-1400 was used for an AX study while CL-1600 was a L-1011 TriStar Twin study in 1973. Note that CL-1401 - 1499 were bulk assigned to the ADP (Skunk Works), perhaps to avoid these recurring TDN "doubleups".
So we can see the Skunk Works sometimes using conflicting TDNs, but they are not necessarily evidence of a separate scheme, or the main Lockheed California department wouldn't have cared about the CL-1200 "double up".