Yes, you have to be quite careful with that method. Also, always make sure to protect the feet and legs to prevent marks or scratches; I usually place a folded towel or similar piece of cloth on the table surface and a thick, folded piece of paper between the torso and legs. I try to use different methods if the figure or parts are particularly rare, valuable, or more likely to be damaged (which is definitely the case with leg parts with printing on them).
For customising, I try to use the Fi?ures heads almost exclusively, so I would support more use of them in sets too (but the new My Fi?ures sets seem a bit light on parts for the prices).