"Up", "down", and "over" aren't adverbs. Frequently they're prepositions, but in verbs like "set up" they're just part of the verb itself, since "set up" can't be understood by the meanings of "set" and "up". (See http://en.wikipedia.org/wiki/Phrasal_verb for more info).

And also: what on earth is the author proposing the methods be named then? Rename "setupInstance" to "setInstanceUp"? In what way is that clearer or more readable? And really, "setup" and the like have become verbs through usage already. Which would you be more likely to say?

1. Can you set a new user up for me?

2. Can you setup a new user for me?

For me, #1 sounds awkward, #2 sounds more natural. Similarly for cleanup, teardown, and other common computer tasks.