1- pip freeze will miss packages not installed by pip (i.e. Conda).
2- It does include all packages, even not used in the project.
3- It just dumps all packages, their dependencies and sub-dependencies. Even without conflicts, if you happen to change a package, then it is very hard to keep track of dependencies and sub-dependencies that need to be removed. At some point, your file will be a hot mess.
4. If you install specific platform package version then this information will not be tracked