Couple of questions about the fbx export process.

If I have a geo object with multiple objects inside of it, it seems that File/export - Filmbox FBX - exports everything as a combined mesh. Is it possible to preserve the objects as individual meshes on export?

I noticed that having multiple geometry nodes at the scene level exports each one without combining the objects. However with multiple objects inside a geo, they just get combined. thanks in advance,

Try going to the /out context and dropping down a FBX output ROP. There are additional options available using the node compared to using the File menu.

Easiest way is probably to make sure each geometry piece lives in an obj level node (use Object Merges if necessary).
Put them all in a subnet and export that. Unity will see it as a model prefab containing those different objects, each with a transform.