1. The meaning of 'freckle' is VERY narrow. It simply means the color deposition in small spot in the skin. I initially (after seeing a drawing by using dots to make a face barely standing out of the background) used '若隐若现' but I think that I use too much imagination here and I am going to change that interpretation. With its strict meaning we will run into a logically difficult situation--how fickle things necessarily become freckled(斑点, 色斑)?
2. If your explanation is right the next word 'with' is out of place. How the properties or attributes after 'with' fit in your explanation? Are they only pertain to the thing that is 'freckled'?
Before I write this comment I googled 'Whatever is fickle, freckled (who knows how?)'. The second and third hit seem to support what I mentioned about the sentence structure. I think the poet used nouns and noun phrases in his poem. 'Whatever is fickle, freckled' is a noun phrase, or two noun phrases if we like to say this way.
Below are the quotes from my googling:
"suggest that diversity among humans is just as beautiful as it is in nature and is created alike by God, and should, therefore be respected and appreciated. Interestingly, Hopkins applies some adjectives that were used about his poetry: "original, spare, strange." These oddities, along with his turning of "fickle" and "freckled" which normally suggest a negative judgment to a positive connotation, are used, instead, as evidence of the infinitude of God's creation."
--http://www.enotes.com/homework-help/what-gerard-manley-hopkins-praising-why-he-329360
'Line 8
Whatever is fickle, freckled (who knows how?)
?This line gives two more adjectives to add to our main adjective, "dapple."
?Surprise, surprise, they begin with the same letter: "fickle" means something that changes a lot, and "freckled" returns to the topic of spots or dots.
?In other contexts, "fickle" can be a negative quality in a person who changes his or her mind too often, but in nature, fickleness brings about new things at which we can marvel.
?In parentheses, the speaker voices his private wonder at how all these things acquired their "pied beauty."'
--http://www.shmoop.com/pied-beauty/stanza-2-summary.html