If you really, really can't modify existing build targets can you just let that dev web.config pass through and either detele to overwrite it latter, or just ignore it dependiong on deployment process? Say by making additional build target that will be invoked only in projects that need that cleanup? I'm pretty sure that you can find several places in your build where you can do a cleanup.
Alternatively you can inject a target earlier in the cycle to copy your master web.config to where you need it - the modality depends on your actual situation - there's no universaly best way to do it.
The issue is not going to dissapear if you just say "I don't dare to touch anything". You'll have to modify something either by making new target to copy, or clean up or by copying or cleaning up before/after the build.
You could also make 3 variants of the _CopyWebApplication - one that does everything like out of the box, another that does everything except trying to copy the file(s) no one wants and one empty - so you are not forcing anything but providing options.