A standard Strat style trem cover has either 6 holes or a rectangle cut out. This is to give access to the trem block when you are installing strings on a strat style bottom loading trem or hardtail. Most companies that use trem covers probably buy their trem covers from the same manufacturer as Fender... so they use the same design. The holes are useless on a Floyd Rose, and you don't need them. They do serve a purpose on a Stratocaster with a bottom loading bridge (Tremolo or hardtail). So, no... you don't need to include those holes when you make a custom cover.