I can't comment on the historical development of this practice and whether it might have arisen from confusion with ogonek. I think the library on our center has IJAL from its inception (nearly 70 years), so I could jump back a decade or two or three to see what I can find out. In the mean time, how is U. of Chicago Press to migrate their publishing of IJAL to use Unicode? Either they encode a bunch of base-ogonek characters (most of which would still need to be proposed) and use fonts that maintain "poor typographic practice" of having ogoneks that look like retroflex hooks, or they need to revise their typographic practice and switch to using typeforms with real ogoneks. The former has obvious concerns, but the latter doesn't remove all concerns -- the legacy practice continues to haunt. As I have looked through various sources, it has been apparent to me that authors/editors/publishers often endeavour to maintain original typography in quotations. So, with a bunch of base-ogonek characters encoded, it will be unclear to them how to represent quotations from IJAL.
Peter, I often suggest this, and you rarely take me up on it, but I for one will not try to debug this kind of discussion in plain text without seeing all the actual glyphs. PLEASE write a discussion paper with a series of examples from a series of publications, illustrating the practices and the problems, and then we can all be informed enough to make recommendations. What "a bunch of base-ogonek characters" could mean is a mystery to me.
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Michael Everson * * Everson Typography * * http://www.evertype.com