My first at-home Mac was a 6100 DOS-Compatible. After about three months I took the useless 486 card out and put in the way too tall 8100 video board and ran it topless for years. If you want a Zip in there, get a SCSI ribbon with another connector on it and just lay it on top of the HD with the top off when necessary.

Alternately, if you don't have a video (or whatever) card on it, mount the Zip in the big horizontal card hole on the back. It'd be just like the SD slot on the back of a MacMini, only 20 years more primitive