I would suggest against starting with a root of c:\ -- I would recommend retaining the "subfolder" of "simutrans", just like the current downloads.
2) Users may not want files at c:\simutrans
C:\ was just used in this example, it could be c:\games\simutrans or anything else thats decided. Also when you double click the exec it opens a dialogue box that can be changed to anything. In this case it would say c:\ if the user then added my transport games\ it would unpack to c:\my transport games\simutrans.
For different paks it could just be made as Simutrans\pak64 or simutrans\pak128 etc. but this will, I`m sure be discussed and decided on.
Another advantage is that it can(or not) automatically over-write existing files, so as paks are updated, so would the users installation be.
Simusetup automatically installs to c:\program files\simutrans, maybe that might be considered. Personally, I prefer not to put games in there as in explorer there are so many folders in \program files it takes ages to navigate to simutrans, but thats just me
I don`t know if this would work for Linux and Macs, so it`s probably all academic anyway.