I have same frame and mine sits the same. I bough everything from speedtech knowing it fit and wouldnt have to micky mouse finding and trying 100 differnt combonations.
The way you have it installed is Correct and it is sitting in the designed location. when we were designing the system there were many things to consider. We built some 1.75" rear offset mounts for my Nova and it really started to cause problems with all kinds of things here are a few.
steering shaft to header
depending on which drive system your using
alternator to frame and motor mount
Rack to Block
P/S to frame
Then there was the little issue of not being able to remove the transmission with out removing the subframe.
The trans tunnell needed to be modified ( as you found out)
There will always be compromise when designing things and customer ease of install needs to be at the top of the list.
We mounted the motor in the most ideal location, for as many reasons as we could conceive.
Not to say that is can't be moved as we have done it on my car but you need to know that there will be other issues that you will need to contend with if you choose to go down that road.
I tried those initially but they would not fit with the oem F-body accessories. Could not mount the alternator. Had good luck with there DD (double D mounts) that have 3 positions- forward/nuetral/back