Well I can tell you what I know so far, and this isn't meant to bump or promote anyone in particular.
www.wecinlay.com ~ Recommended by some members of this forum in older threads. Told me via email that making for PRS SE guitars is not a problem. However between Korean, Indonesian, and Chinese made SE's there may be size differences. Also I've read it said that some SE guitars have USA sized truss rod covers. Will find out the specifics. Seems to be the most accommodating to customers' customization needs. Offers black & white, and colored. Uses ebony, rosewood, and koa for the covers.
www.thaliacapos.com ~ Offers a handful of options. Uses ebony, rosewood, and koa for the covers. Offers
This Size Chart to print out to the right size/scale, and you can place your existing TRC on the paper to verify exact size and fittings.
www.philadelphialuthiertools.com ~ These ones are plastic. Specifies USA PRS, Indonesian PRS SE, and Korean PRS SE sized offerings. Was not able to tell me where Chinese made PRS SE sized TRC's stand amongst these, but I will find out the best I can. Engraved. Engraved signature. Color imaged TRC's.
I will use that Size Chart soon and report my findings so the info that might specify sizes of USA core and SE's made in Korea, Indonesia, and China can be here for use by others.