the FARs actually define major and minor if you search through them, the problem then becomes the interpretation of the definition. I do not have the actual definition in front of me but the jist of it is any modification that can affect flight characteristics or structural integrity is a major.
I have actually been in the same situation before during a prebuy, a shop fixed the firewall and some other panels and structure on a brand C, they did a full sign off in the logs but did not do a 337 for the major repair. when I confronted the shop they said the FSDO ok'd the repair as minor because they used a factory firewall. they were partially correct in their thinking, using factory parts for the repair can eliminate the 337 requirement in some cases. in this one, they also manufactured other panels during the repair. those manufactured panels required that a 337 be filed. the FSDO did not support the shops position when the full repair was evaluated.
in the case you talk about above, the repair station has the authority to repair and modify the item IAW an FAA approved repair and operations manual. becuase this has been aproved by the FAA the IA has no authority to override the repair station unless he can show the repair is not airworthy and causes an actual danger if operated in that condition.
I hate to say this, but because there is so much interpenetration of rules, regulations and repair manuals standards vary. what one person won't accept another would, the big question is did either look at the actual limitations or is it just their opinion?
Brian