So, to be perfectly honest, it doesn’t seem to me that there is any real difference between a Skill Proficiency and a Tool Proficiency, they just seem to be categories of Proficiencies and Proficiencies seem to just be equivalent to 3.5e Skills. Arguably the main difference being that in order to use a Tool Proficiency you need to also have a piece of gear, the Tool, used for that proficiency, is all.