Just because Chaos is a constant threat does not means it important in the grand strategic level at all. The Orks are much more of constant and continual threat. But even both combined, are nothing to internal conflicts.If Chaos were something that could be stomped with brute strength the Imperium would not be in the state it is in, it is nothing if not good at stomping.
The biggest problems the IOM face is it lack of fast FTL communication. That lets corruption in and I am talking old fashioned skimming of the top to decorate your house corruption, delays military response, etc. The layered systems the IOM use of escalating response serves ok, but really we should change the IOM up into about 40-50 Segmentums to further decentralize power, and reduce the overal communication lag.