Can I configure it to be placed in the same location (C:\windows\something) that .msi files produced by windows installer are hidden in, instead of in C:\Porgram Files\MyAppFolder\?
Also can I change the name to something more obvious in intent than unins000.exe?
The uninstaller path can be changed by setting a value in the script file:
[Setup]
UninstallFilesDir={win}\Installer
There doesn't appear to be a way to change the name.
With the shipping InnoSetup there is currently no way specify the Uninstall file name.
Since Source is available you can change the behavior the file name is stored in UninstallExeFileName and is set in GenerateFilenames() in the Install.pas