The ghetto way--
Since all the setup floppies are, is a collection of single-file compacted .cab archives (which can be expanded with EXPAND.EXE), it is possible to dump them all into a directory, and pair that directory with a batch file that expands them all sequentially.
You would need:
The setup floppy diskettes
A means to get the contents of the diskettes off of the diskettes, and into a loose pack folder.
A bootable diskette with fdisk, format, sys, edit, and expand on it.
More time than is really healthy or wise
A sense of radical or reckless disregard for propriety.
The basic process:
The boot floppy is used to create, partition, and format (with system) the hard disk. (Assumed CF card)
Remove the hard disk, and attach it to your selected means of manipulation, to get the loose pack folder on.
Within the loose pack folder, there is a batch file you will have to write, that calls expand.exe on each and every compressed file, and supplies (manually) the correct expanded name.
This batch file creates a directory (if it does not already exist) at C:\DOS.
It expands every file in the loose pack folder.
It copies a cleanup batch file into C:\DOS
It copies a generic config.sys and autoexec.bat to the root of the drive
It chains (via CALL) to this batch file
This new batchfile "deltree /y" the loose pack folder.
Echos to the screen that you need to reboot.
(If you are especially lazy)
Set up the DOS environment inside a virtual machine, and have the VM change the disks. (VirtualBox I know for certain allows for this.)
Use disk image handling programs (like winimage) to get access to the freshly minted C:\dos folder.
Copy the dos folder out to someplace you can reach it.
Boot the afore mentioned minimalist boot diskette on the target.
Partition, and format with system, the target system.
Attach the prepared drive to your main working machine
Copy the C:\DOS folder on.
Create minimalist Config.sys and Autoexec.bat
Profit.