Avirah- Yes, there are times when we say Tzarich Iyun, but why should we say Tzarich Iyun, when there’s a simple explanation. The most logical thing to say is that Rav Shlomo Zalman knew about Rav Kook’s controversial views, and while he may not have agreed with them, he did not feel that they Passul him from being a Gadol. He probably took into account, also, the fact that Rav Kook was very poetic, and did not mean these statements in an absolute way. It seems much more logical to assume like this, rather than leave it as a Tzarich iyun.
You make the assumption that “one Gadol’s Tzadik can not be another Tzadik’s Rasha”, and based off this, assume that the Gedolim who were Machshiv Rav Kook were misguided. This would then mean that Rav Isser Zalman, Rav Tzvi Pesach Frank, Rav Aryeh Levine, Rav Boruch Ber, Rav Elyashiv, Rav Shlomo Zalman, Rav Yaakov Kamenetsky, The Tzitz Eliezer, Rav Ovadya and many more Gedolim were all misguided. Wouldn’t it be more logical to say that Rav Elchanan was misled (i say this with the upmost respect for a huge Gadol)? As i mentioned before the letter Rav Elchanan writes is clearly based on the premise that Rav Kook supported Keren Hayesod, something which we know now to not be true. It seems therefore that the letter you’re quoting from Rav Elchanan was based on false premises.
Your assumption that “one Gadol’s Rasha is not anothers Tzaddik”, to begin with is questionable. Gedolim do not have monotheistic views on everything, and that is part of the beauty of Torah. Because one Gadol held one way is not a reason to say that all the other Gedolim were misguided and really would have agreed.
You mentioned Rav Boruch Ber, so i’ll just mention that he writes a letter to Rav Kook in which he praise him very highly calling him a Tzadik and “kohen Tzedek”.