I don't think the article is suggesting ever making temporary copies of data into a structure-of-arrays (SOA) format. Rather the choice should be made at design time and you write your code accordingly for those parts that deal with SOA data.

The author's advice is that you should go with the standard array-of-structures (AOS) format by default, but if you know you'll be doing number crunching, use an "unrolled by eight" grouped SOA format that's both SIMD- and cache-friendly.