Your facility is likely using Vol III for its surgical or procedural registry; thus, some level of accuracy is demanded. Personally, I have advised hospitals for years to convert their registries over the CPT, as some very large US hospitals have done; with ICD-10, my suggestion is moot. Though I agree it is superfluous, there is little you can do. I have regularly seen hospital bills produced (paper primarily) with both sets of codes, but no DRG for the OP bill type.
To respond directly to your question, if you must code in both, CPT bundling rules do not impact the code assignment in ICD-9 Vol III. In other words, you cannot (ever) apply the rules in one coding system to another coding system; they are distinct and unrelated--hence, why crosswalks are so very inaccurate, they do not account for variances in coding guidelines. You would probably need to code the procedures separately in ICD-9 Vol III, though I do not have my manual here with me as I respond to this.