I generally use WBPP with the following caveats:
1) I use a SBIG camera with TheSkyX/Voyager combination. I need to remove the PEDESTAL keyword to get good results. I use a script to do this before doing WBPP.
2) I do have data sets that don't completely align using WBPP. In those cases, I have to manually do registration if I want to use whatever subs failed.
3) Probably more often than not, I manually redo the integration step. As per the warning, I frequently find I can get better results if I tweak this step. For example the WBPP script does not give access to the Large-Scale Pixel Rejection parameters that can be a great help in getting rid of airplane and satellite trails. I also find I want to fiddle with the pixel rejection parameters fairly frequently to optimize my result.
Still, even with those caveats, it takes enough of the tedium out of things that I find it worthwhile. And it is useful to have the final integrated stack from WBPP even if I don't use it, because I then have that as a comparison to try and do better.