Before Windows 95/3.x, there was DOS.
There were no rules in DOS, or r_x permissions like Unix.
The DOS kernel itself didn't really impose any structure on the filesystem. All that mattered was:
- The two files that comprised DOS itself (MSDOS.SYS, IO.SYS) had to be "inode" 0 and 1 on the disk in early versions,
- the kernel parsed \CONFIG.SYS on boot, and I think looked for \COMMAND.COM if you didn't specify a different shell with COMSPEC= in CONFIG.SYS. There were defaults if \CONFIG.SYS didn't exist, but of course all your DEVICE= stuff won't load and you'll probably not have a working mouse, CD-ROM, etc.
\AUTOEXEC.BAT was optional. That's it. Any other files could be anywhere else. I think the MS-DOS installer disk put files in C:\DOS by convention but that was just a convention. As long as COMMAND.COM was findable DOS would boot and be useable-and if you mucked something up you just grab your DOS boot floppy with A:\COMMAND.COM on it and fix it.
From what I recall most installers-if provided-made a directory in \ and put all their files there, mixing executables with read-write data. There was no central registry of programs or anything unless you were using a third party front-end.
Windows 3.x and 95 inherited the DOS legacy there.