I believe it's a limitation of BSP. It's likely one of the very reasons why users tend to go with model-only levels because they work around this issue and offer tons of other advantages. The best that can be done for blocks, however, is to build transparent areas as a map entity then set the map entity's alpha to whatever. This affects the whole object though. Using the overlay flag may not work with BSP, but I haven't tested this so I don't know for sure.