Addendum
Hi RG3/Director
It seems highly unlikely that the FDA will not have encountered the current interpretative disagreement before. If so a quoted precedent will probably be shortly forthcoming. Their Compliance Guides are probably being pored over at this moment. 
It is interesting to scan the 1995 Final Rule (attached below) for "allergen". There are no hits.
“Allergens” are also not mentioned anywhere in Ch.19 of the F. Guide’s 1st ed (1996) issued to parallel the Final Rule.
Fish and Fishery Products - Final Rule.pdf 876.9KB
68 downloads
As far as Prerequisites goes (aka SSOP from FDA’s POV at that time) the details within the document illustrate the then-existing argument as to whether Sanitation should be haccp handled by CCPs or not. By 1997, the NACMCF (afaik the basis of FDA’s thinking) clearly favoured Prerequiste programs (although not specifically defining allergen control as such), eg –
http://www.fda.gov/F...06801.htm#app-a
There are IMO 2 hazard scenarios involved here as far as allergens are concerned –
(a) the hazard to a consumer from a fish-X product regarding it’s intrinsic possession of an allergenic fish protein (does it?) or other X constituent allergenic proteins,
(b) the hazard from cross-contamination from this fish-X product/its process to other products which do not contain the fish allergen.
The Fishery Guide’s “not suitable” comment seemingly refers to (b). I infer it considers that (a) should be a CCP and controlled by labelling.
Unfortunately, from the Guides POV, there is (at least in 2011) no relevant supporting content within the Final Rule to enable the F.Guide to “upgrade” its "not suitable" opinion into a stated action.
I deduce from RG3's posts that the (Prerequisite?), allergen control Program (including labelling control) covers both (a) and (b) ?
From an FDA POV, it is interesting to note that The Guide is literally that. Some extracts from the Intro. -
(i) FDA announced its adoption of final regulations to ensure the safe and sanitary processing of fish and fishery products in the Federal Register of December 18, 1995 (60 FR 65096) (hereinafter referred to as the Seafood HACCP Regulation).
(ii) This guidance is also intended to serve as a tool to be used by federal and state regulatory officials in the evaluation of HACCP plans for fish and fishery product.
(iii) FDA’s guidance documents, including this guidance, do not establish legally enforceable responsibilities. Instead, guidance describe the Agency’s current thinking on a topic and should be viewed only as recommendations, unless specific regulatory or statutory requirements are cited.
(iv) Processors may choose to use other control strategies, as long as they comply with the requirements of the applicable food safety laws and regulations. However, processors that chose to use other control strategies (e.g., critical limits) should scientifically establish their adequacy.
It’s an interesting thread.