In the pictures i've seen, the back of it is flat except for two holes that access the rotor bearings or retaining bolts or something like that. Not sure I see the holes you're referring to. Are you talking about 2 oclock from the bypass hole, and another at 3 oclock on the other side of the partition?
If those are indeed holes, they would be poking into the right side rotor shaft access hole as I described above. If memory serves, these are sealed holes from the back face of the blower. Unsure if that'd make a difference or not. Doubt it. If those holes aren't sealed then I suppose it could cause a small oil leak behind the motor or perhaps a tiny vacuum leak in the right circumstance. Still seems like something that a dab of JB weld would fix without too much problem.