fwiw. I'd echo what Mark Manley suggests - other than the size/weight of the engine these bikes are exactly the same size, so if you're confident with the seat height and ergonomics, go for the 500 (actually 471cc) twin, as it is a far more relaxed motor on the open road, and still very fuel-efficient.
While you could certainly get by on the 300 (286cc) single in typical Central and South American riding conditions - that is presuming you plan to stay off any interstate style multi-lane highways anyway - you might as well go for the more relaxed torque of the twin cylinder version. In either case, both of these engines are well-proven as reliable, low-maintenance and very economic with regard to fuel and servicing costs - so either would provide the ideal 'travel' platform regardless of which chassis you have them fitted to.
As for luggage accessories etc. have a look at what some of the aftermarket suppliers from Thailand offer (where these bikes are assembled, and are also more popular in general) - you can get a luggage rack which replaces the rear/passenger seat pad (note. the pillion seat is standard on the 500, optional on the 300 in the US), and there are also windshields designed to fit this bike too, if that is something that you feel you might need.
The only real limitation with these bikes is the comparatively small fuel tank compared to their sister models the CB500X and CB500F (and R), but in practice you ought to see around 200 miles from a tank unless you are pinning the bike at full throttle - so perhaps another reason to go for the 500 twin?
Personally speaking, I think the way you describe setting up the bike with some all-terrain tyres* and some sort of skid plate and simple luggage system would make for a very nice low-seat all-road touring bike.
*Just be aware that the wheels are 16" front and rear on these bikes, so your choice of alternative tyres is going to be more limited.
Have fun!
Jx
ps. I just had a noodle at the US Honda website and they do actually offer OEM luggage accessories including both a rear rack and a second rack to replace the passenger seat pad, and also saddle back frames - albeit I imagine those are for their own bags, although they could probably be used to support a one-piece throw-over saddle-bag style bag too (Giant loop Coyote etc.).
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