Difference between masterwork tools and skill boost item?

I have a player who wants to buy masterwork tools as opposed to buying magic items that boost his skills.

The reason being, masterwork tools grant a +2 bonus to a skill and cost 50gp.

Magic items that grant bonuses to skills cost (bonus) squared x 100, meaning a +2 magic item costs 400gp.

So i guess my question is…. what is the difference between a masterwork tool and a magic item that grants the same bonus? Are there certain skills you cannot have tools for? Was that the intent?