From what I've found it won't hurt performance, mileage or any of that good stuff by covering the intercooler also, at least in my experience. I run mine with 2 flaps closed, which seems to be the best balance between warmup and EGT's in the ambient temperature range I experience (about +10°F to about +40°F). If the ambient temperature changes significantly or if the load on your truck changes (i. e. go from running around empty to towing) you'll simply need to adjust the flaps accordingly in order to keep coolant temperature and EGT from becoming an issue.
***Edited to clarify the above***
If you like to run the truck hard empty for performance reasons, you might find the need to adjust how many flaps you have closed. It will raise EGT to some extent, although in winter at least on the ~15-25 mile trips I usually make the mileage gains resulting from having it warm up quicker offsets any mileage penalties from higher EGTs. It can be a tradeoff but IMO it's worth it for quicker warmup time and ability to keep it at operating temperature more effectively.