Occasionally I'll see a mileage run where even with paying for a positioning flight it is a good deal.

Given that I am looking at international mileage runs, if my positioning fight is late and I miss my international flight I'm in big trouble.

My understanding, however, is that if the flights are in the same PNR you are protected against an misconnect. Is there any way of getting the positioning flight into the same PNR and having the system give you the broken fare (rather than the through fare which might be higher)?