There is a point penalty when you use an Imperial Bot to destroy a structure. The penalty differs depending on: 1) what you destroyed, and 2) which version of the game you’re playing.
In the mobile versions of the game, the penalty is a multiple of the final point value awarded for the structure. E.g., making a House awards you 1500 points, and the penalty is either 1x, 2x, or 4x that value. In version 1.21 the penalty multiplier could either be 2x or 4x (the 4x was due to a bug). I believe that the bug was fixed in version 1.23, so that all penalties in versions 1.23 and 1.24 are 2x. The multiplier is also 2x in versions 1.34-1.36; however for versions 1.54-1.63 the penalty multiplier is 1x. As of versions 1.73-1.74, the penalty multiplier remains 1x for most structures but is 4x for Castles, Floating Castles, and Triple Castles.
If the structure is a “super” structure (made with more 4 or more of the lower component) then the point award was 2x the award for the normal structure, and the penalty is based on the increased value. E.g., building a Super House awards you 3000 points, and botting it penalizes you based on the 3000 value, not the 1500 value.
As far as the penalties go, the history of how a structure was built does not matter. E.g., the penalty for botting a Super House is the same 3000 points times the 1x, 2x, or 4x multiplier, regardless of whether you made your Super House with 4 Normal Huts or 5 Super Huts. Use of Crystals in the building process is not factored in, either.
On these platforms, rather than using a multiplier, there is now a hand-picked penalty for each type of structure. E.g., building Bushes and Houses awards you 20 and 1500 points, respectively, but botting Bushes and Houses penalizes you 40 and 4000 points, respectively–the first happens to be 2x the award, but the second happens to be 2.67x the award. Again, we don’t factor in the history of how a structure was built; the only thing that matters is whether the item being botted is currently super or normal.
Botting of Castles, Floating Castles, and Triple Castles is not allowed in these versions of the game. More information on this can be found here.