I agree, that is an unforgiving design and we apologize for the inconvenience. I don't believe your missing anything and you have clearly identified the limitation down to a physical chassis fit issue. As stated, it an experimentation at best from what we had to go by. I can't recommend the chassis modifications as i don't know what other problem could come up or that it would be a good fit.  It would be completely up to you to continue experimenting, but i would suggest calling it a valiant effort and return the parts.  Let me know if you have any further questions.  
I am purchasing a used R410 for home use, and believe it is of the cabled hard drive configuration, and not hot-plug/swap.   While this is not a HUGE concern, hot-swap is nicer.   Looking at the chassis pictures (and the system maintenance manual, i can't seem to tell if it is possible to convert the cabled configuration to hotswap.   Is it possible to do this, assuming I purchase the backplane, hard drive trays, and a H200 controller?  Thanks!
Can a Poweredge R410 with cabled drives be upgrade to support hot-swap by 
adding the hot-swap backplane and a H200 Controller?