I'm no expert on this. And I haven't installed an IMSB myself. I will offer one thought and others will weigh in I'm sure on the technical details.
I can't believe that properly torqued IMSB flange bolts would extend through the engine case so as to interfere with the crankshaft. If such interference were possible, then it would be a terrible design. I can fully understand, however, your concern. The consequences of installing the IMSB wrong are bad.
Hope this helps. Let's see what the true experts have to say.
BTW: here is the latest set of installation instructions:
http://www.lnengineering.com/imsretrofit.pdf