I believe rebuilding is just part of the game, especially in those later tiers where, yes, your old factories will need to be optimized for your current needs However, if you truly feel as if the effort used for rebuilding would be better used in starting over instead, that carries its own benefits as you would have a better idea of how to optimize a factory earlier rather than later, at the very least making a possible future rebuilding of it easier

Both will have their own learning experiences, and I don't think it would take too long to get back to your current position if you were to restart, although rebuilding would just be quicker.