It's hard for me to believe that the housings aren't straight and if they are off you need to straighten them. I have done 10 or so housings most D60's cut them down and weld on new ends and when my friend ran late model stock cars we did a lot of 9" fords.
If the axle slides in nice without the o-ring on the outside of the bearing then it will work fine and wont ware out the bearings or cause a failure, and if you look at the ad that you posted for green bearing it ask what inner seal do you need, no where does it say leave them out. I'm just saying. I just cant see the point of leaving out the seal.