As mentioned by other commentors, there's not currently any good reason to use parts other than drills, both types of wheel, and one magnet in the final design.
It's possible to use pistons to get one extra space by pushing your drills into illegal positions (doing it more than once makes your machine stop working), and it's worth doing that because you can get rid of the pistons afterwards. The pistons would be worthless if not for the exploit, since they don't actually save any space. It might be a different story if they got buffed by extending further; maybe if they auto-retract at the end of the run so as to not be cheaty?
Also, having infinite storage for ore and extra coal-fuel seemed odd. Probably cap fuel to the max instead of letting it roll over? Alternatively, a storage part for ore might be a practical limiting factor for longer runs.
I feel like there ought to have been a real use for the structure parts, to stop stupid-looking designs from being optimal. Maybe make most parts have to attach to something 'solid' to work? So frames, fuel tanks, pistons, and maybe ore storage makes up the 'hull' of your digging machine, and every other part needs to connect to one of those parts in order to be legally placed.