Hey ALIEN, welcome to Blender!
It’s supposed to work with the option clamp overlap, with the bevel tool as well as the modifier.
Looks like you’re using Blender 2.78. I tested with version 2.79, which is out btw :), but the overlap still happens. It works fine with the buildbot development version from today, though, both modifier and bevel tool. So if we get a 2.79a update, it should then be fixed.
You can try the daily build from buildbot, but keep in mind that it might contain other bugs. In my experience those builds are usually fairly stable, though, at least the official 2.79 ones from the first section. Link: https://builder.blender.org/download/.
If you want to make the buildbot version self contained so that it uses its own settings and you can try it safely, extract the zip somewhere and create a directory named config like this: <blender dir>/2.79/config, alongside the folders datafiles, python, scripts that are already there.
Have fun, I hope it helps.