Shiny and new in "vehicle mode", yet battle-damage re-appears in "robot" mode

Transformers and logic don't really go hand in hand, Bay's version being one of the worst culprits.

But if I were to give it a guess I would say that they maintained the shiny exteriors as part of their disguise. Bumblebee quickly changes from a beatup (but classic!) Camaro into a brand new modern one in a matter of seconds. When they are in robot mode they don't need to put up the facade, so I guess they conserve energy by not sprucing themselves up.

Just stumbled across this, and thought about it in relation to computers.

Here the primary objective is not to preserve energy, but rather to preserve time for processing instructions. You know this from any computer you use. If you run several programs in parallel, the processing time gets shared between them, and they all run at a slower rate.

This could easily be the same with the transformers. They have to use processing power, to remain in the vehicle-state, because they constantly have to "execute the look_as_car() method" or whatever.

As robots they look like themselves, and therefore they have all 100% of the processing power, to use for moving, jumping, dodging, whatevering around the place...

Yes as you said,

...they operated at a very low (molecular?) level...

this could be the explanation. They would have recreated themselves damage-free somehow. But if this is the case, I don't know why they just don't do away with those damages when fighting as well..

Personally, I think its just a plot inconsistency. If the transformers are that advanced as to recreate themselves as a vehicle at a molecular level, they should also be able not to sustain any damage when fighting.

Also, I'd say the obvious reason during filmmaking is that it's product placement for the latest generation of cars they want to show off. If they're damaged with battle scars, it wouldn't be very effective ;)

Another flaw, however, is why not just transform into a battle robot that's slightly less beaten up than their current selves? Energy conservation, I guess, but if that makes you slightly less likely to lose an arm, surely that's a good thing...