It depends on what you intend to do:
1) It very much affects performance by introducing additional draw calls, if at a single skeleton you have to switch often between two or more materials, as explained here.
2) If you are using only Additive and Normal blend modes, it can be batched in a single draw call when using PMA blending. Thus it is not creating additional draw calls.
3) In general, a lot of overdraw is not beneficial for performance (I assume this is what you read regarding mobile performance). However, the Spine runtimes always render skeletons in back-to-front order to provide proper alpha-blending at borders of Attachments. If the runtimes used cutout (0% or 100% opacity) shaders and front-to-back order, Attachments would look very jaggy at their borders. So in any way, Spine is already performing alpha-blending here since it is necessary to layer 2D images nicely. Note that especially for some mobile devices alpha-testing instead of alpha blending can also incur a performance penalty, so it is the draw order that is the main overhead here.
So in short I don't think that using blend modes in your scenario will affect performance in a too negative way, but as always: please perform some measurements on the target devices under a typical gameplay scenario to be sure.
