Warmoth make up to order within the standard Strat outline. Tell them you want an S-X-S (X meaning no pickup). They will also do any standard pickup sizes: Tele, P90, humbucker, even Dano and Filtertron if you ask, You can do this with controls too: V-T-T is the standard Strat config, but if you want a X-V-T or even X-X-V or V-X-X they'll do it.
Just be aware that not all Strat replicas have identical pickguard outlines and you may need to change the position of a few screw holes. When in doubt, try one of the custom makers (like Pickguard Heaven
)and send them a tracing.
I usually make my own oddities by hand, but it's a helluva big job - a days work. The custom manufacturers use CAD/CAM stuff to whip out a pickguard in a few minutes - most of which is setting up the options).
BTW, I saw some interesting Mighty Mite pickguards at Bothners recently - pearl red (both dark and bright reds), pearl blue, pearl green, etc. You would have to be carefully choose what would work with a specific guitar colur, but some nice possibilities if you get it right.