This doctrine can't possibly apply in this case, because something that is inside a locked safe deposit box can't possibly be in "plain view".
Based on reading what appears to be the judge's actual opinion in the case (I've posted a link upthread), the excuse the FBI offered, and which the judge accepted, was that they had to open the boxes in order to "inventory the contents". But they also said they would only search the boxes to the extent required to identify their owners. From what I can gather, each box was contained in a "sleeve" which, in many cases, had a form in it, that could be read without opening the box, that identified the box's owner. Since each box was locked, the FBI could have simply made an inventory that, for each box, said "one safe deposit box, number #X, locked, contents unknown", with an additional note that either said "form found identifying box owner as A", or "no form found identifying box owner".
In other words, the FBI relied on an inconsistency in the warrant: it said they did not have permission to seize the contents of the boxes, but it also said they could follow "standard inventory policy", which in turn contained provisions that could be interpreted inconsistently to both require an inventory of the contents and to only authorize a search to the extent needed to identify the owner, if possible. This certainly seems to me to violate the Fourth Amendment.
In the case of boxes which were accompanied by a form identifying the owner, what obviously should have happened was that the FBI should have done nothing more with those boxes until the owner could be investigated to see if there was probable cause to think they had put evidence of a crime in the box. If there was, an additional warrant could be obtained to search that box. If not, the box could just be returned, unopened, to the owner. (In fact, the boxes of many plaintiffs were returned during the course of this lawsuit--but not unopened.)
In the case of boxes which were not accompanied by a form identifying the owner, the question would be whether that in itself was probable cause to think the box might contain evidence of a crime. In any case, that would be a question to be properly addressed by applying for an additional warrant.
So I think there were several rights violations here: first, the judge who approved the warrant should have spotted the inconsistency in what the FBI was asking for and resolved it; second, the FBI should have adopted an inventory policy that was consistent; and third, the judge in this ruling should not have let the FBI get away with what they actually did.