I'm afraid you probably won't get a definitive answer on this one. Other posters have pointed out the advantages of one transit type over another. IFR means we can lock you on a heading and at an exact level, without worrying about you needing to dodge IMC, which usually makes separation against other IFR traffic straightforward. (Unless you're very slowly transiting the missed approach / departure / overhead at less than 1000' above MSA, in which case it's hard to issue a safe level to departures or go-arounds beneath you).
On the other hand, VFR vs IFR requires no separation, merely traffic information to both (plus avoiding action to the IFR if he requests it). Without having to achieve 3 miles or 1000', this often allows a more efficient use of airpace for everyone.
Planting my bum even more firmly on the fence, there are probably a host of other possible reasons why the examples you quote occurred! Your best bet would be to try to arrange a visit to the ATC unit involved and chat to their approach controllers. Take biscuits and be prepared to be talked at for absolutely hours....