If you look elsewhere you'll find I'm also currently trying to sort the same problem (see Equipment section).
I'm finding that all the Peli cases seem to be really numb sizes (but I've yet to follow up the suggestion of looking at the Explorer cases).
Drills tend to be incredibly awkward shapes to fit any container efficiently.
You could keep your ears to the ground for anyone scrapping a neoprene diving drysuit with a waterproof "personal zip" fitted to the lower abdomen. (Top tip - wash the zip as it'll have been used for something unpleasant!). If you cut out the short personal zip leaving a wide flange of neoprene you can then use additional neoprene to build a neoprene dry bag which will be waterproof. You need to pad any sharp edges of the drill or other contents of the bag to avoid the bag being punctured. I used to take a Bosch drill through Far Sump in Peak cavern this way (385 m long and 8 m deep; a good half hour swim when heavily loaded) and it never let me down.
An alternative DIY remedy is to make a drill bag from a wagon inner tube (along the lines of the old carbide "pigs" that people used to make for expeditions before proper lamps were invented). One end is cemented permanently shut (best done by compressing it between two sheets of wood in a vice as the glue cures). The open end needs to be significantly longer than the drill such that it can be folded over several times and secured with inner tube loops stretched over it. Again, padding for any projecting drill edges prolongs the life of the inner tube carrier. I've also used these for transporting things through sumps so, in a normal caving situation, it will not leak provided you avoid punctures. Old towels make ghreat5 padding as they soak up any minor leaks of water which may occur. Trawling round any grubby caving hut will normally generate a plentiful supply of nasty old cast off towels.Best thing is this costs nowt.
I've never used Ortleib type waterproof bags but I know people who have and they seem happy with them.
Hope that helps.