The best way to handle the configuration is to implement a standard serial port on the floppy controller processor module that is already implemented in the FPGA. Connect these lines to a serial port on the Amiga side, and you now have a simple communication system between the low level floppy controller and Workbench. From there it should be trivial to write a bit of code that lets you copy files from the Amiga side over the serial line to write it to the SD card. The Amiga should see the floppy controller as a floppy drive from one direction, but should also see the floppy controller as a remote computer connected over the serial port not even realizing that they are the same processor.
While writing the floppy controller code would likely be limited to a small subset of programmers, the Amiga side of things could be handled by a much wider range of developers. As a bonus, the floppy controller could have a second serial port exposed to header pins so that an adapter could be made that allowed external control via simple DIY projects.
As for bundling extra information, the best way to handle that is to adopt the RP9 file format from Amiga Forever. This would not only give you your image files, help files, manuals and whatnot, it would also allow you to store you Amiga configuration file in with the rest, all in one file.
As a seperate task, if the disk controller serial connection described above were implemented, the disk's startup file could be set to auto initiate a download of the various files from the serial port to a ramdisk. This means that all of your supporting files would be available to you on Workbench from the same RP9 file.