Technic 8858 Rebel Wrecker alternate model impossible to build?
Welcome to LEGO Answers! That's a great question. 

I don't actually have this set, but I believe the issue is that the linkage piece that you are using comes in two separate variants:



The variation is subtle, but the small flanges that you mention in your question were added in a variant that came later than the set you are trying to build. This is what prevents you from connecting ball joints from different sides, and is one of the cases where part variants are not equivalent for particular building scenarios. You really need to use 2739a here rather than 2739b.

Hopefully you still have the original 2739a parts around, but if not, you can pick them up on Bricklink relatively cheaply.