I wonder if it's possible to set up a "drive" (SD card in this case) with both FFS and FAT32 partitions in a way that both the Amiga and a PC will recognize... I guess the boot sector / partition table will be a problem.
I went a slightly different route with my 3000, and got the Buddha IDE adapter instead, with an IDE - CF card converter. With the right mountlist, that lets me mount FAT32 formatted CF cards without any trouble. (Well, except that the Buddha doesn't do hot swapping, so there's a bunch of rebooting / power cycling.)
But I guess in your case that won't do you much good unless the 3000 still has another SCSI drive that it can boot from and can copy data from the SD card to.
Of course my preferred way to copy data to/from my Amigas is over the network, with both the 3000 and the 1200 having had Ethernet cards since the 90s, and they know how to mount my NAS so that's all nice and seamless, just not very fast.
An X-Surf 100 card is almost 150 euros, though, so a bit steep just to transfer some data once in a while.
I guess what I would try is see if I can set up a serial port link between the 3000 and a modern computer and transfer the data that way. That should be a fair bit of tinkering and not very fast. But: cheap. At most a couple dozen dollars for a serial to USB adapter and maybe a cable. And although slow, it can run mostly unattended for arbitrarily large files without having to set up WinUAE and/or swapping SD cards or USB flash drives.
Another networking option that is easy and more affordable is
PLIPBox, which is an Ethernet adapter that plugs in to the parallel port of any Amiga (the A1000 needs a special version). I think it's about $50 on Ebay. About 10 times faster than serial and 5 times slower than real Ethernet.
Yet another option: use
WinImage or a similar tool to write files to a bunch of images on the Gotek USB stick, then mount those images on the Amiga and copy the data one at a time. Of course that would require some trial and error to get PC disk images on the Gotek to mount on the Amiga, and you may need to use another tool like RAR to split up large files and later stitch them back together. And keep changing virtual floppies on the Amiga side. I suppose there must be a way for the Amiga to talk to the Flashfloppy software on the Gotek to select a new image...