That’s a nice looking printer what is it?
If you bought my hardware kit you should print the taller z motor mount. linked here http://www.vicious1.com/blog/parts/
As for height, Yes you should do the legs through the table, a 10″ z will probably make cutting aluminum unbearably slow. If you try it make a box so you can mount your wood and material as close to the gantry as possible.