Well its used as storage and had a lot of similarities to a normal chest, its just looks and opens differently to a normal chest... they probably grouped them up with chests for less clutter in the creative inventory.
Second this, each tool material has its own weight for enchantment with gold being the best. A good example is you can get a level 5 efficiency on gold and iron picks on a table but not on diamond ones. There's a good amount of info you can look into via the Minecraft wiki enchanting page to help for future refernce...
I might have a solution to what is happening, the monster spawners have a larger dedection range than you would think (9 blocks from centre), and if too many skeletons are too close it the spawner it won't spawn any more or have a very slow spawn rate (i learned this the hard way making a zombie/drowned farm myself). So in that regard i think everything is working as intended... all you would have to do is extend the path before the skeletons fall after the bubble elevator so that they are out of range after they drop so that the spawner just keeps pumping them out. Of course this is only the case if you are letting them build up before you kill them, if you are killing as they drop its less of a problem and spawners can be naturaly be slow as well...
I hope this can help you and your troubles.