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You have one instance per (big) program. If on Linux or Windows you run two copies of UAE and in first one you start "Lightwave" and in second one you start "OWB" then you have memory protection between them. Crash in one, doesn't affect the other.

In the video (with keyboard shortcuts) each time you see a new Amiga-style window appear a complete new OS instance gets "booted"/started and some program (incl. Doom 3 hw accelerated) within loaded and launched. There's only one (big) program per instance.

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You can have 32 bit versions of the OS instances and 64 bit versions which you can mix however you like. You can have 10 big 32-bit programs each using 2 GB of RAM. So that already gives you more memory. 64 bit compiled programs would run in 64 bit OS instance and get you much more memory per program. 64 bit can still be same old compatible API incl. fast Forbid/Permit, etc.

multi core: between OS instances you get it for free (run 2, 3, 4 copies of UAE and Win/Linux will share cpu load among available cores. "OWB" may run on core #1, "Lighwave" on core #2). For programs themselves inside the OS instance there are multiple options: simplest for something like a raytracer is to launch render tasks as new/additional OS instances. Or have option for OS instances to be launched in multi-core safe way (for multi-core safe new programs) where necessary OS incompatibilities are activated (doesn't matter as you only run one big compatible program in it) like no Forbid/Permit (or very slow Forbid/Permit), no relying on hi-pri task never beeing run side by side with lower pri task).