Q1) As it sounds to me, when using 'make', it treats each of the two items listed before (encourages networks; encourages lack of social boundaries) as independent concepts, meaning one doesn't require the other to validate the remainder of the sentence.
- Technology encourages networks that make operating in hierarchies problematic and challenges traditional ways of doing and managing work.
- Technology encourages a lack of boundaries that make operating in hierarchies problematic and challenges traditional ways of doing and managing work.
When using 'makes', it seems more as though the combination of the two is what makes the final argument true.
Q2) As for this one, I see what you mean, and while the answer is yes, it's important to consider which is the better option. To begin, if I were to make that same modification, I'd also put it as: "...that makes for problematic operations in hierarchies." What comes to mind is the manner in which the sentence will be delivered. If it's spoken, like a line of dialogue in a film, then your alternative structure is fine, so long as the person voicing the line does so appropriately, maybe with subtle annunciations to reflect the atypical format and to clue the listener in to where each fragment of the ordinarily-expected sentence could be identified.
Otherwise, and especially in writing, it's really a matter of intuition: if a sentence feels right (doesn't require rereads; has a flow to it; is read easily; is interpreted both easily and correctly; entertains the reader rather than irritates them; etc.), then by all means get creative. I've gotten heartfelt thanks from Professors who appreciated a novel twist I'd added in my schoolwork when otherwise the students had adhered to a more bland and literal approach. It's just my opinion, it's acceptable -- so long as it's done right.