There's nothing to stop you from having a scratchplate as you first envisaged. You could fit a 'standard' one if you had pots and a jack socket with long enough shafts. Alternatively, like my Ibanez RG-08 has, you could cut bigger holes round where the knobs and jack socket go for the knobs to fit through.
But by now, your mental picture of what the guitar will look like has probably changed as well. Just a thought.
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