The BIOS generally will run Config.sys and Autoexec.bat when it "boots" the machine, since it has to get any drivers that aren't "permanently registered" before it can read the drives and get the "rest of the story" about how to start.
Windows pretty much "flushes" the "boot" installation of Autoexec.bat, but will re-run Autoexec.bat when it starts, if it's there, since this is the only place you can put in a call to start drivers needed by "non-compliant" hardware. It can be used to start odd-ball (non-Windows) programs you may want running, but there are usually better ways to do this "inside Windows."
Most people never see the "Windows run" of Autoexec.bat because it's usually a "zero-byte" file, i.e. empty. It's there for those who might need it, but in normal Windows operation it really isn't much more necessary than a third thumb.
If you have installed Windows on a machine that has "legacy" hardware - stuff that doesn't have "Plug-and-Play" capability, you may need a driver for it in Autoexec.bat, so you need to be careful about randomly taking stuff out; but the "run-twice" thing is sort of built in. (You may also be able to find a newer driver that will let Windows start the old hardware.)
You don't say what "cleanup" you feel is necessary, but one way to get it out of running twice would be to put it in a separate .bat file and put an icon on your desktop so that you can "click to run" after Windows starts. You may have to tell it to run in a DOS window in Win95 or Win98, but later versions of Windows do it pretty much all for you.
There also are ways to put a "run-once" file into Windows Startup, that would likely do it for you automatically at each boot, but it's not something I've done recently so I'd have to do some lookup.