Info store question:
Yes, the exmerge does have to read from the Info Store (if that's what you
meant by IS) for each PST. 

Time Frame question:
No, not at all. Actually the Exmerge utility goes very fast. We have a 6.5gb
DB and that takes about 20-25 minutes to do a Exmerge on it. Also, you do
not schedule the Exmerge at same time, I would say run the exmerge during an
off-time and clock it. We are setting our time to do exmerge 1 hour before
backup goes off. Then PST are written to a folder and the rest is history.

Backup Question:
You do not do the exmerge at same time (see above). As far as extra time?
What ever your through-put is on "X gb's" of data, then that is the time
that the backup will take in excess.