Typhoon, the EAJA would likely apply when all was said and done, but there's a chance it wouldn't - and also a chance you'd lose the case, even though the merits seem obvious to us. In any event it'd take years, and the jurisdiction of such cases isn't always nationwide. Another district could go after another pilot and start the entire process over!
IIRC IRS wasn't applying the merchant seaman interpretation to pilots until relatively recently. I certainly never got pulled over for it. I'd be interested in knowing the stateside homes of those getting correspondence. It's possible this is, for now, one or two rogue districts (or just some "rogue agents in Cincinnati"

).