Hi Thomas!
Glad the tips were useful to you.
Yes, it is amazing how "travel" (not the cycling part, but time on transport and elsewhere) can mark a bike in myriad small ways.
I'd say if the scratches are small and "clear" -- non-rusted -- then you should be safe to leave them, but I'd check periodically to see if that's still the case. If they start to get rusty as with the ones you've treated, then you can always sand them clear and touch them up later.
A little story:
A close friend owned a used-bike shop for 25 years and would save his crash-damaged frames for me to dismember for the tubing and for "autopsies"...and to learn about rust! Key areas to watch are around bottle bosses and cable guides. Salty-sugary-sticky-acidy energy drinks from water bottles can be the culprit and so can dripping sweat that is salty and remains in contact with the surface for awhile, long enough to breach the surface treatment or find scratches to develop rust in the underlying steel. Similarly, the bottle bosses on the underside of the downtube can be vulnerable simply because of water and mud flicked up by the front tire and the area is hard to clean, so it remains damp for an extended time.
Also, water can enter the frame around the seatpost and cause internal rust. Keeping the seatpost well lubed can help there, as can a short length of tire innertube stretched over the seat lug. Up front, water can run inside threaded steerers and down the outside of threadless ones. depending on how a frame is configured and vented, a small bit of tape over the vent holes inside the head tube can prevent water from entering the top and downtubes by that route. Thorn have done a *really* good job (by design!) of arranging the placement of frame vents (needed to allow hot gases to escape during framebuilding) so they are not open and exposed. It is a small but very thoughtful element that adds greatly to the live of their bikes, so it can take years to fully appreciate. I've had to manually plug some of the exposed vent holes on my other bikes with little dabs of kneaded beeswax (manipulated beeswax is waterproof but breathable to a degree and is moldable and won't flake like raw beeswax). If you do plug a frame's vents, be sure to first treat the interior with oil, cavity wax, or FrameSaver, as once again humidity helps rust to go wild, and the interior of tubes don't have much air circulation and if water collects inside, rust can get a foothold pretty quickly.
Amazingly, unless you live in a seacoast climate or ride where roads are salted, there is generally enough chromium content in quality bike frames they don't seem to rust much *if* they are outside and allowed to dry after they get wet. Put them under a tarp or awning where air circulation is compromised, and they can almost flash-rust compared to ones sitting outside. My bike shop friend used a semi-trailer for extra storage and the bikes inside it rusted (humidity) as did the ones outside under the trailer floor. The ones stored out in all weather were almost untouched by rust in comparison. General humidity makes a difference, also. I bought a remarkably nice 1972 Windsor Professional racing bike for USD$20 from a fellow living in the high desert plateau of Central Oregon who stored it outside 'cos he had no room in his small cabin. It failed to sell at two garage sales, so sat outside through two very snowy winters sometimes completely buried under powder snow. There's almost no rust on the bike's Columbus tubing, thanks to the generally low humidity in that region.
Similarly, I have quite a few lengths of raw frame tubing in my garage. That stored in the factory cardboard boxes had better be oiled or it can develop freckles of surface rust. Longer lengths standing exposed and upright do fine, as dampness can't collect.
I've enjoyed reading your blog entries and found familiar places from my own tours described in it.
All best wishes for happy travels; may your Adventures always be of the best kind.
Dan.