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FRUA has a resource manager built into it so that it swaps things in and out of memory as they're needed.  That might be difficult with an RTS, but something to think about.  It's always been the more impressive thing to me is how people manage to squeeze so much into such limitations of memory.  These days, developers are just like 'meh, they can buy more ram.'  well, maybe not so much now, since ram prices are insane...

I'm doing something similar with FRUA and Ultima VI.  But I'm also targeting Falcon/TT first, then going to try and get them running on an ST.
The reduction to only requiring 4mb of ram seems pretty required, since normal hardware is kind of maxed out at that (without adding in something like a pistorm, etc).

Still, it's hard to believe you got that to run even in Hatari in ST mode, plus with that good of sound!  Insane what the AI can do these days...