For what it's worth, minification and obfuscation often refer to the same thing. Advanced minification in Construct also does a lot of obfuscation, merely because almost all variable/function/property names get renamed to short, meaningless names. In this sense it's both smaller and more obscure, so it is both minified and obfuscated.
If a third-party addon does not work with advanced minification, contact the developer and ask them to fix it. It should be relatively straightforward to support, and we have documentation specifically covering it.