Wazou: I’m not sure I agree that there’s a problem in the image you posted. I’m interested to see if I’m out of touch here.
To your question about tool vs. modifier: the code for the two is almost completely shared, and I will push to keep the two feature-equivalent.
cgstrive: I suspect that the problems with Bevel-after-boolean are a combination of: (1) Boolean problems; (2) the fact that Bevel currently doesn’t do anything about cases when the bevel causes edges to move past other geometry (overlapping), unless one uses ‘clamp’, which itself is not perfect at calculating the right clamp value.
For problem (1), that is out of scope for this GSoC, though coincidentally it is my current personal project to improve Blender’s Booleans, and that may fix some of those problems. For problem (2), I think this is likely too hard to fit into the time we have for GSoC, but maybe there are some simple cases that could be made to work.