I have not read through all your text because in my eyes, it is not necessary. 

Your core question is stated in the headline. 
And the answer is: it does not matter which instance (original or clone) is 
missing.
Clones shall protect against data loss on the backup media. However, as long as 
there is one instance left, the save set is valid of course (same savetime).

Your other question in fact is: will the pool option to "store index entries" 
speed up the backup?
And the answer is: maybe. If the index entries are in the size of the file size 
and you have a huge number of files, it will be obvious.
But test yourself and find out. Only you know your environment.

Now you have to judge whether you can afford to live without CFI data during 
recoveries.

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