Let custom flags use version aliases

[ibobgunardi]

Fixes #2229.

When a root command defines its own flag using the default version names, setup now leaves the custom flag in control instead of appending the built-in version flag and treating that value as a version request.

Tested with:

• go test . -run TestCommand_Run_(Version|CustomFlagCanUseVersionAlias)$ -count=1 -v
• go test . -run Test(Command_Run|_Version_Custom_Flags|CustomHelpVersionFlags|Command_CanAddVFlagOnSubCommands) -count=1
• go test . -count=1
• git diff --check