I find sometimes needing turning the entire QCTP at an angle to the top-slide; e.g. to suit a particular tool geometry or more often, when the slide has to be rotated to allow the tailstock closer to the work.
That would be negated by machining the tool-holder blocks or moving the stud so the blocks can descend past the slide-surface.
The simplest solution is to use smaller tools, or machine down the height of the ones you already have!
(We should remember these lathes were designed when it was normal to stand the tool directly on the slide surface, or at best, to use a basic 4-way tool-post with a fairly thin base.)