If there is no way to alter the installer and the configuration so that it works with different paths there might still be a way: Sandboxie.
It's originally meant for isolating software from the operating system but in this case it could allow for multiple installations. However, it's not just a simple change of a path setting so you might want to read into it at: http://www.sandboxie.com

The installer will only let me choose the directory to put the basic installed files in. Once I boot up the program, no matter where the main file (engine.exe) is located, it always writes to that superfluous directory.
Thanks for the suggestion, but Sandboxie seems a bit too complicated to boot up every time I start the game. Also, I'm running on a laptop with severe overheating issues, and running that much gunk at once might shut me down.

Its just something you are going to either have to learn to ignore or avoid games that do that which there are alot now. Civilization 4 does the same thing as do a ton of other games. Its how alot of these games have been programed to work with the windows user accounts so if more then one person uses a pc they will have there own saves. I hate this myself but there is nothing you can really do about it.
Also make sure that your running games with administrator set in compatibility or installed to somewhere other then program files otherwise saves usually end up in the virtual store as well.

Hey,
sandboxie is really rescource efficient. It just sits in the background and idles. On my machines it takes 0% CPU and only 1,4Mb RAM so it shouldn't be a problem of rescources for you.
Also it's not complicated to run a software with it. When you have the installer you just right click and select "open with sandboxie", install it to a sandbox and then you just run that program within that sandbox. There are a few tutorials on the site.
However, like I mentioned, it does take a little effort to get used to it - but once you are you'll certainly like it. It's perfect for older machines as well since you can remove software 100% when you install it to sandboxes and thus it will help keeping the system nice and tidy.
Sorry for not being able to help more but this is the only way I can think of, aside from running a VM but that is absolutely out of the question if you're working with an older machine.
Regards,
nu.