You are correct in that the CCI edits list 69990 as inclusive and will not allow a modifier to override the edit. Medicare has identified few surgical CPT codes where they will reimburse separate for the use of the operating microscope in addition to the surgical procedure. Medicare will not reimburse under any circumstances for the use of the operating microscope in addition to the laminotomy CPT code 63030.

However, it is not incorrect coding if the documentation supports that the operating microscope was brought into the surgical field to perform microdissection or microsurgery.

Per the AMA CPT Manual, the instructional guidelines identify which procedures include the use of the operating microscope, thus CPT code 69990 would not reported in addition to any of the procedures listed. You will note that CPT code 63030 is not identified in the list of procedures that include the operating microscope.

Operating Microscope (69990)
The surgical microscope is employed when the surgical services are performed using the techniques of microsurgery. Code 69990 should be reported (without modifier 51 appended) in addition to the code for the primary procedure performed. Do not use 69990 for visualization with magnifying loupes or corrected vision. Do not report code 69990 in addition to procedures where use of the operating microscope is an inclusive component (15756-15758, 15842, 19364, 19368, 20955-20962, 20969-20973, 26551-26554, 26556, 31526, 31531, 31536, 31541, 31545, 31546, 31561, 31571, 43116, 43496, 49906, 61548, 63075-63078, 64727, 64820-64823, 65091-68850).

2008 AMA CPT Manual.  American Medical Association. 2007. Page 298.