Arbortext Editor and FOSI formatting do not recognize non-proprietary processing instructions. FOSI formatting for Arbortext PIs is discussed in a 43-page section in Chapter 11 of my book Practical FOSI (available for purchase at Practical FOSI). PDF of the book's TOC, LOT, and LOF is attached, as well as PDF of the TOC for the section on PIs.
Maybe a supported PI would work for you, but there is no need for that; it just adds unnecessary complexity. Your best bet is to code the gentext in the e-i-cs for elements in the document.
Note that with FOSI formatting, the source document is never altered in any way. FOSI formatting is a batch, black-box process that creates only machine-readable files. , No formatted version of the source document is created that can be modified independently from the source document and then output. With FOSI formatting, there is always only one source document, which ensures the integrity of the content database..
Suzanne