I personally don't think the intention was to ever allow failure on two separate rolls as can greatly increase the chance of failure. However your point is well taken, I didn't really think it through. If you do use two separate rolls you are correct, you can't just ignore failures on that second roll because they could be modified failures, not just a UM 1 or 2.
But I think that one single roll is the way to go, with two different bonuses applied. This way you have a flat 2% chance of an UM failure. For the SCSM, if not automatic, you add in your bonus and determine success or failure. If that succeeds then you add/subtract your directed spell bonus, or your BAR mod. That modified result could also fail.
If you consider a case where there is higher chance of failure on both the SCSM and on a modified BAR, then using two rolls can *greatly* increase the chance of failure as you can fail on either or and the success rate is a conditional probability. However with a single roll your highest chance of failure is still going to be only the highest fail rate of either the SCSM or the BAR (alternately the SCSM or the EAR).