I put a clear Strat-style pickguard on a rear routed Warmoth body last fall. The end result was great though, as you'd expect, there are some challenges.
First, Warmoth's rear drilled standard strat control pattern has the same spacing as you'll find on a Fender Strat, but they are drilled in a slightly different position (down and a bit askew). This means a stock strat pickguard won't work if you have Warmoth drill the holes. It won't work even if you want to use an undrilled standard size pickguard and drill it yourself. The lower 'horn' isn't long enough or wide enough to allow for lowest 2 knobs.
If you drill the holes in the body for the controls yourself to try and use a standard, drilled strat pickguard, I still don't think it'd work due to how close the lowest knob is to the edge of the body and how the control route is cut. I think Warmoth drills their strat controls slightly askew the way they do so that the control pot is far enough away from the edge of the body to allow for the mounting of the rear control cover plate.
The easiest option would probably be to get an undrilled body and an undrilled pickguard. This way you could be assured that all the controls would fit both inside the body and the pickguard.
The second problem is the combined thickness of both the body (inside the control cavity) and pickguard has to be taken into account so you can physically mount the control hardware. The thinnest clear acrylic that I could find was .080". Using this, I had to thin the wood of the body a little bit inside the control route so the pots and selector switch could be mounted. I did this with a Dremel and a grinding stone attachment. Took probably 10 minutes. Stock 3 ply pickguards are .090" I believe. These would probably still work OK with some thinning to the body, but I'd seriously consider a thinner, singly ply guard. The 5 way switch is the biggest issue because if the body/pickguard combo is too thick it won't properly engage the first and fifth position. The really cheap 5 way switches (not the super switch) have a longer lever that works just fine with the thicker guard but they limit your wiring options.
The control holes on my body were drilled stock by Warmoth so I ended up having Terrapin Guitars in Oregon make me a custom transparent pickguard (shown below). I simply traced out the shape, pickup, knob and screw hole positions I wanted on a piece of paper and Terrapin digitized it and cut it out. They did a fantastic job and everything lined up perfectly. NFI of course.