The oldest edition of the CFR I have available is 1996, and that definition of “chief mate” is in there and is the same. It only appears to be recent as it really had little effect in the past. When OSVs were all less than 3,000 GT (1,600 GRT) there was no way to meet the requirement for an “unlimited” license to have at least 50% of service on vessels over 1,600 GRT. You could not be the chief mate on any vessel over 1,600 GRT without holding a license as chief mate unlimited. When OSVs became larger than 3,000 GT, that changed, but it was not until the 2013 rule change that formally authorized an OSV endorsement for 1,600 GRFT/3,000 GT or more that anyone took notice of the definition of chief mate and the service requirements for master unlimited, even though they had been there for a fairly long time.
As far as checking COIs, you are mostly correct. NMC evaluators definitely go into “MISLE’ the Coast Guard’s database that includes vessel data. Note on almost all NMC checklists there is a note “check MISLE.” Will they always check the COI? Maybe not. If manning isn’t an issue for evaluating sea service in the application, probably not. But they will still be in the system to check things like vessel tonnage, and possibly whether the vessel is authorized for voyages on the routes described in the service letter.https://www.gpo.gov/fdsys/pkg/CFR-1996-title46-vol1/pdf/CFR-1996-title46-vol1-sec10-103.pdf