EAP distributions should remain consistent no matter which distribution channel was used to obtain it. Installer can alter EAP distribution in several ways:
- optional packs (AppClient, Docs)
- adding management user
- runtime environment configuration (logging, socket bindings, ... + quickstart examples)
- shortcuts

Apart from these, EAP after installation should remain as clean as possible (close to clear unzipped EAP).

Running EAP installation with some runtime configuration option included, leaves plenty of files which should be cleaned up before installation ends:
- Uninstaller and installation directories are fine
- icons directory should be present after installation only if user choose to install shortcuts
- mgmt-users.properties file differences is reported as JBEAP-1777
- several directories should be removed - domain_xml_history, host_xml_history, standalone_xml_history, auto-start, kernel, log, servers, data, vfs
- reordered elements and removed comments in configuration files are fine (these are done by EAP)

See attached dist-diff report for complete list of differences

We can split this one into more issues if it works better for you.