Another part of the equation is the bridge pup rout, as it looks like you'll have to modify it a fair bit to fit the pup if you use the forward bridge position. And once you do that they'll be no going back, literally.
As Gav said, the end grain of plugs is pretty tough to hide. I'd recommend putting a few plugs into some scrap wood, something close'ish to body's wood colour, and testing the effect of the DT colour on the plugs vs surrounding wood before making a decision. It may be that embedding a bit of coloured Timbermate (coloured with DT stain, or actual rosewood dust) into the end grain of the plugs could help them to blend/match. Experiment before committing to irreversible changes to the body.
Edit: Also, with that type of 'drill press' frame the tensioning bolts tend to strip and slip, so beware. There can also be a fair amount of play and wander with the drill tip once you start drilling. Practice first on thick scrap wood, as accurate string-through holes are not easy. One thing that can sometimes work if you have an overhanging bench is to clamp the press to the overhang and have the workpiece/body on another bench under it, so you're not restricted by the press' throat depth. You would need a long drill bit and may even need to reverse the press by removing and inverting the press' handle/body on the shaft/pillar so the base is at the top of the shaft. If you can wrangle it into a useable position it could overcome some of its limitations. Another alternative is to mark the string through holes onto the body and then sit the press on the body but drill down through the hole in the centre of the press' base. Hard to do, but may be more stable.
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