Why do Alu repeats form secondary structures?
Single-stranded RNA can easily form secondary structures, a very important example of this are tRNAs. 

From a quick look at the article you read it seems that these Alu repeats work similar to riboswitches in the 5'-UTR. They can form secondary structures that block translation initiation, riboswitches commonly do this by hiding the Shine-Dalgarno sequence in a stable helix.

This kind of regulation of translation can obviously only work in the 5'-UTR as that is the place where the translation starts. The 3'-UTR can't affect translation in this way as the translation starts at the other end of the mRNA.

The Alu repeats still can form secondary structures in the 3'-UTR, and the article suggests that those might have an effect on mRNA stability.