mmmmmmm. Another option for hybrid CDs is to image them on something modern using a tool that produces bin/cue files. It's just about the only way to get, say, BeOS-oriented CDs to work at all. Unfortunately, that reduces the ability of older computers to work directly with those image files, but it does improve the accuracy of imaging and you can put them on a modern computer to turn a real CD. If I remember correctly, MacSD might work with bin/cue files as well, but I'd have to go look.
It seems like in general, third party OSes and games is where this is going to go weird, but there are things like dual-platform copies of AppleWorks 5 and how you manage those depends on whether you want an accurate image or a functional one, for my part I'll admit it doesn't bother me the idea that a dual-platform copy of apleworks 5 got distributed separately, but.