My experience was different. I regularly saw multiple CLINs referenced in Block A. I never even considered the issue of identifying which CLIN in Block A to be about billing. It was far more important to ensure the correct distro statement/ instructions for preparation was applied to the particular data being procured.
As it relates to your original question, the monthly status report should be its own deliverable with its own CDRL. Reference all applicable CLINs in Block A (for example: 0001 -0002 (0003 if exercised)) ... but not because of the billing question, but because the monthly status report would have its own distro statement and instructions for preparation versus the other CDRLS on the award.