As far as I'm concerned, there are two options for space-saving motorcycle travelling: Motocross boots & flip-flops, or normal bike boots that are comfortable enough for some walking/hiking. (There simply isn't enough space to accomodate for 2 pairs of shoes/boots).
In the end, I went for the later option and got myself some waterproof "Altberg Hogg" boots. They've got a good reputation and are sturdy enough around the ankle areas. Altberg also improved the design, so shifting gears doesn't wear out the laces anymore (my mate Charles had problems with the old design). The only real downside of the Hogg boots is: they don't offer any shin protection, but I'll find a way around that. Maybe some MX-shin protectors?