I think it's generally acknowledged that in the WC universe, letters designate variants of the same design (F-44A from WC1, F-44G from WC2) whereas roman numerals designate entirely different designs which simply share a previous design's name (WCM - Rapier I, WC1/2 - Rapier II)...
Therefore, a Rapier IV would be the fourth design to ever use the Rapier name, while the F-44G "Rapier II" would be the seventh variant of the F-44 "Rapier II" design.
It's kinda like how the A-10 is the Thunderbolt II, with the P-47 being the original Thunderbolt... and how the F-8 (I think) is the Corsair II, with the F-4 being the original Corsair. Each of these four designs also have their variants which are represented by letters (F-4U, P-47D, etc)
--Eder