Sounds like a lot of thought was put into the I/O locations. I didn't know there are two analog in jacks. It makes sense - one rear for permanent connection and a front one for temporary. I personally am not bothered by the sub out being on the back even though I will be frequently connecting and disconnecting my sub. I am just glad there's a sub out.

House of the Rising Sone
Out in the mid or far field
Dedicated mid-woofers are over-rated