1. Understand, as Ramchal makes the point, that the idea of there being two “accounts” maintained in Heaven, a transcendent and often unreadable “Mazal account” and a more tangible and explicable “reward and punishment account”, was largely unknown in the past, and by even some of the greatest souls . We’re told that even Moshe himself wondered how things could often be so puzzling, and how the righteous might suffer ignobly and the wrongful could go along unscathed (see Berachot 7a) . So our “not getting it” shouldn’t surprise anyone.
That’s because G-d “hid the higher form or governance” based on Mazal “from His created beings” until later (i.e., with the printing of the Zohar and the revelations of the Ari and his greatest disciples). So when the ancient prophets spoke about one thing or another in the realm of Divine Justice and the like, they only addressed what they themselves saw in the Heavens without being privy to the full picture.
2. But we’re also to understand that “even those times that G-d wants to govern the world within the Mazal system, He still and all has things come about in such a way that … it would fall within the reward and punishment system, too”. For “whatever must happen, will happen”, under one or both systems.
That implies a number of things, though: that a lot of what happens in the world is largely inexplicable and ironic; that a lot is a blend of apparent right and wrong, or fair and unfair; that a lot of what happens to us seems to be garbed in a mixed-message, if you will, from Heaven; and more.
3. Summing up the matter Ramchal reiterates that at bottom, “(G-d’s) governance is in truth rooted in the (eventual) perfection of all of creation.” It is the main point of creation which everything else is a mere supporting detail of; as absolutely everything acts to move the universe along in that direction. It’s just that there are various inscrutable rules involved in this process, to be sure, along the way.
And while reward and punishment certainly factors in to a very great degree, still and all the Mazal system is the ultimate mitigating factor, though the two do work in conjunction.
 For Kabbalistic references in this chapter see R’ Friedlander’s note 479, and R’ Shriki’s notes 167 and 167*.
 The idea that there were things associated with Jewish Thought that Moshe wasn’t privy to is highly controversial. After all, didn’t Rambam say that the Moshiach will draw his ultimate knowledge from Moshe’s Torah (implying that Moshe was in possession of the ultimate revelations), yet the Zohar declares that R’ Shimon Bar Yochai (who came later than Moshe) was aware of things that Moshe wasn’t.
The notion of ongoing revelation — of there having been revelations subsequent to the giving of the Torah on Mount Sinai — that’s implicit in the latter idea is a point of heated debate among Torah sages until this very day. Suffice it to say that Ramchal himself clearly implied that the Kabbalistic authors and insights that he drew upon were examples of revelations that Moshe and other earlier sages were not exposed to.
Rabbi Yaakov Feldman has translated and commented upon “The Gates of Repentance”, “The Path of the Just”, and “The Duties of the Heart” (Jason Aronson Publishers). His works are available in bookstores and in various locations on the Web.