That's exactly my point--it doesn't cover it up, it exposes it. If the store is doing something wrong in one of those other processes and then filling the resulting holes in the floor using some other tool, say just SUBTing when they find an out, then the store is less likely to realize there's a problem. If, on the other hand, they use EXF--which then shows up on a report--it will be easy to see that something upstream is not being done properly.
It's also more efficient than SUBTing everything individually, doesn't have a negative effect on DTK metrics like OUTS/RSCH w/Locs, is more predictable than shooting a manual CAF or POG fill (where you never really know what's gonna come out), etc. As long as you make sure people are only using it when it makes sense--and someone is pulling the Pull Type Report every week to keep track of how often EXF is being used so they can see if there's a problem--then there's no legitimate reason NOT to use it.
Not allowing the use of EXF is throwing the baby out with the bathwater.