Learn English – What does “to leap intellectual chasms in a single bound” mean

It's describing God (I assume, judging from the capitalised Me), and using the analogy of an onion's layers.

If you take away the outer layer showing mercy, expecting to find cruelty underneath as the true nature, you don't: you find mercy. And if you scratch at that layer to get underneath, you find mercy again. He is mercy all the way through.

In this case, beauty is more than skin deep: it is the entire being.

There are actually two factors here:

1. Modifier ambiguity. You're correct that "whole" can be interpreted as modifying either both "society and the religious world" or only "society". However, the natural interpretation (in my opinion) is certainly the former. To say the latter I would explicitly prefix the sentence with "both" ("both the whole of society and the religious world"), in which case "are" is certainly correct.

2. Collective noun. Is "the whole of society and the religious world" being treated as collective noun? In other words, is the impact described happening to the members of society or to the structure of society itself? If it's the former, then it's normal in British Englishto use a plural verb despite the grammatical singularity of "whole of"; otherwise, you should use a singular verb. In American English, meanwhile, a singular verb is expected in both cases.
   
   This point is best illustrated by the two sentences "My family is big" and "My family are big". In British English, the former would imply that you have many family members while the latter would imply that those family members are obese. In American English only the former would sound grammatical.