There are two caveats I would mention. The first you already know, which is that the speed of your clips increases by 4%, so to keep the length of our piece the same you'll have to re-edit.
The second is that the conform procedure in Cinema Tools changes the original clip - it doesn't make a copy. If you want 2 versions of the clip, make a copy first, then do the 25fps conform on the copy.
Actually, there is a third, which is that in some cases the 4% increase in pitch of the audio can be disturbing. Especially if there's dialog, and some clips are changed and some aren't. If this happens to you, the best thing to do is to pitch shift the converted clip back down 4%. This can be done in Soundtrack Pro (which you also have).
With these considerations, then yes, I think it is feasible to deliver 2 versions of the same material.
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Jesse Rosen
Director of Technical Development
Abel Cine Tech, Inc.www.bustedskull.com