I think it'll work fine on the Atari 8-bit, the external hardware will be under software control (and be invisible if the software doesn't enable it). I'm not using any addresses normally accessible without hardware being added (there's a couple of pages dedicated to external h/w on the XL/XE). As for writing into the 8-bit's memory, all Atari 8-bits already halt the processor when Antic (the "gpu") wants control of the bus - there's a signal dedicated to that (/HALT). I'll have control of that signal too, and as long as I time my accesses to not conflict with Antic, the 6502 won't even know anything has happened. Memory is active however (because Antic needs to read RAM to draw the screen), it's just the 6502 in pause-mode.
I'm less sure about the C64, but have yet to look into it in any great detail. On the ST, everything will be memory-mapped into the cartridge space, so I'm not foreseeing too many problems there.