Hi oldboy
Not a problem, if you were to do any custom change then some finishing small amount of paint work would have to be done, and being black it should not be massive problem, being only the edge would be visible, However I do undrestand that for some its easier to sugest than carry out.
Ok another option which can work very well, how much do you actually need to acomadate the back end of the amp, so for example would the rear feet of the amp over hang the shelf, or would the feet just catch the edge of the shelf, either way at a guess you are maybe looking at 2ins short, even if it is a little more, you can run a battern...and I mean a quality peice of wood or suitable material, not roofing battern...I am sure you know what I mean before any one jumps on me,Anyway you run this battern across the back of the shelf, which would then pick up the feet of the amp, weight would not be an issue, nor would it take much room up, especailly as most units are away from the wall, so this should over come that, as for fixing I do not no the design of your unit but if it is wooden construction then that is a good start, but only you know if this can be done. If you are not sure about what i have said just ask, but hopefully you get the idea, and remember it will not look crap if a little time is taken and the finish is good, fixing it is the easy bit its the finish that matters. 8)