No one is advocating long-term use of ArA; in fact, the labels generally say to cycle off for at least 50 days.
What ArA supplementation achieves is a transient elevation in skeletal muscle arachidonic acid content (the key here is transient! -> one reason for the paradoxical effect on interleukins in the baylor study may be that a compensatory effect on cytokines occurred).
This transient elevation, when presented with the proper stimulus (weight training), can result in improved accretion of local myogenic satellite cells, resulting in skeletal muscle hypertrophy. But you are right, the key is balance. Unfortunately, most bodybuilders supplement high doses of EPA/DHA for years without also accounting for their intake of linoleic acid/ArA to maintain the balance.