Notching or modifying the rear main seal retainer for non-stock main cap bolts is not a big deal.  You do need to be careful in not removing any more material than is absolutely necessary.  I typically use a milling machine to do this but careful grinding with a die grinder will accomplish the same thing.
  

Lorena, Texas (South of Waco)

Here’s another picture of a notched rear main seal retainer.  This one has larger notches so it can use machined spacers between the nuts and the main support girdle.  The spacers or the main support girdle is not yet installed in this picture.
  

Lorena, Texas (South of Waco)

I used a grinding stone in a drill (my die grinder bit the dust). Even with a drill, there's no problem grinding the aluminum rear-seal cap. I did check the fit numerous times, making sure that I did not remove more material than necessary. The cap is now properly seated, and my work looks as good as any I've seen. 

I actually installed a plug in the rear main seal housing bolt holes and covered it with silicone and let it set up before installing the oil pan gasket.  I also cut the clearance for the rear main cap bolts prior to installation.  Made it easier to install the windage tray afterwards.  

JDC