The FreHD ROM allows you to select what image you boot from the FreHD using a menu. I think you would need separate boot floppy images for the Gotek, one for each HD image you want to run.
I thought the original 1000 didn't search for add on ROMs like the 1000A does. You need to load some kind of driver to access the HD with those machines.
Looks like a drop in replacement for the TI SN75185. Their are other manufacturers of compatible chips. It looks like the Holtek chip only comes in SOP-20 package. Digikey sells the TI SN75185DW for $1.44/ea. If you can solder SMT ICs, it should be relatively easy to replace.