Since I seperate by three categories -- CFSWW1, CFSWW2 and CFSHSF (my own air force) -- using a self installer usually winds up the same as making a temporary folder and redistributing, anyway.
I would usually do the same myself unless I'm testing the actual auto-install to make sure it works properly. As this involves a new version of CFS2 each time I do this I try to make sure I get it right the first time.
There seems to be a misconception about self-installers which work on basically the same principle as extracting zipfiles direct to CFS2 or any other sim. The install/extract path can usually be redirected to any location you wish so installing the files to different versions of CFS2 should not matter, even if they're on different drives. What is often unclear with these auto-installers is the location within CFS2 itself the extract path should be redirected to. To install properly they must be set to overwrite existing files/folders so if the person configuring the files got it wrong or didn't test it properly there no way of telling which files are overwritten.
Auto-installers are popular among the CFS community & although some are just as complex they seem to give less problems than those posted for FS. Unless you know & trust the person who configured it I would generally recommend redirecting the install path of any self-installer to a Temp folder so the files can be installed manually.
PS. I configure all the Fox Four files myself as this is something I've been doing for a very long time now & I wouldn't trust the job to anyone else. All our "auto-install" files are configured as simple self-extracting zipfiles. These will either auto-extract by clicking on the EXE file or can be unzipped in the usual way with the right-click mouse options. The auto-install path is set to extract the files to the root directory folder of CFS2 in the default location but this can easily be changed by the end-user. Our policy has always been not to overwrite default files.