I don't know jack about wagons, I didn't even know that they used an intermediate shaft. However, I do know quite a bit about L3 tranny's, & 88-91 hatchbacks/CRX's.
If the realtime wagons do indeed use an intermediate shaft, I wouldn't be surprised if the wagon shared the same diff. as the ZC. I only suggest this because a ZC intermediate shaft bolts up to the Si D16A6 block (which is what powers the wagon.
I don't think that the DX/HF/std blocks have the threaded boss casting on the block. I have a D15B2 block here, and it has no provision for bolting up the int. shaft.
ZC diff's have a larger spline/bore than the US Civic/CRX's so to answer your question using my above reasoning, NO an intermdiate shaft will not fit a US L3 hatchback/sedan/CRX transmission.
I'd like for someone to prove me wrong with hard data on this wagon int. shaft. If it is indeed made for the small spline/bore US L3 diff. then I can order a Quaife for my Civic & retain the equal length axles.