Beings that everything in the head moves on ratio and not 1 to 1 it is good to have a lvl flybar when setting up, does not have to be perfect but perfect lends to consistency. As you said and I stated above, the only important factors in this are a lvl mainshaft and lvl flybar. Having lvl skids, tailboom, and frame have nothing to do with it. If mainshaft and flybar are lvl then you have perfect pitch. On some heli's if the frame, or boom is lvl then the mainshaft is also, but not all, and it is up too you to check this if you want too.
The purpose of the locking tool is to make sure the flybar stays in one place whilst you check both blades, therefore all the lvling is not necessary. Reason for this is the position of the flybar is static and does not change, hence the tool. It is nice if the tool holds the flybar at 90 degrees to the mainshaft so you get 0 pitch with a lvl rotor head.